Expression from transposon-based vectors and uses

ABSTRACT

Recombinant expression vectors are disclosed that include a control sequence for recombinant expression of proteins of interest; the control sequence combines a mCMV enhancer sequence with a rat EF-1alpha intron sequence. Some of the vectors are useful for tetracycline-inducible expression. Some of the vectors contain a 5′ PiggyBac ITR and a 3′ PiggyBac ITR to promote genomic integration into a host cell chromosome. A method of selecting a stable production cell line for manufacturing a protein of interest is also disclosed. Also disclosed are mammalian host cells comprising the inventive recombinant expression vectors and a method of producing a protein of interest, in vitro, involving the mammalian host cell.

CROSS-REFERENCES TO RELATED APPLICATIONS

This is application is a division of, and claims priority from, U.S.patent application Ser. No. 16/286,551, filed Feb. 26, 2019, which is acontinuation-in-part of, and claims priority from, U.S. patentapplication Ser. No. 16/072,180, filed Jul. 24, 2018, under 35 U.S.C. §371, as a U.S. national phase application of United States PatentCooperation Treaty Application No. PCT/US2017/015130, filed Jan. 26,2017, which claims priority to provisional application Ser. No.62/388,391, filed Jan. 27, 2016, all of which are incorporated byreference in their entireties.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been filedelectronically in ASCII format and is hereby incorporated by referencein its entirety. Said ASCII copy, created on Mar. 3, 2021, is namedJUST51DIV1_SL.txt and is 36,499 bytes in size.

BACKGROUND Field of the Invention

This invention relates to recombinant production of proteins inmammalian cells.

Discussion of the Related Art

Industrial scale production of therapeutic proteins by recombinantexpression in mammalian cell culture is a relatively recent endeavorthat strives for the greatest possible recombinant expression efficiencyand product quality characteristics that meet or exceed regulatoryguidelines.

Recombinant protein therapeutics offer distinct advantages over smallmolecule therapeutics in specificity, dosing frequency, and generallylower toxicity. (Catapano, A. L., Papadopoulos, N., The safety oftherapeutic monoclonal antibodies: Implications for cardiovasculardisease and targeting the PCSK9 pathway, Atherosclerosis 228:18-28(2013)). The number of recombinant protein therapeutics has increasedgreatly since the 1980s when this class of therapeutics was firstintroduced. Despite their advantages, the cost of recombinant proteintherapeutics impedes access to most of the world's population. (Moon, S.et al., A win-win solution?: A critical analysis of tiered pricing toimprove access to medicines in developing countries, Global. Health7:1-11 (2011)). A number of strategies to reduce the cost of recombinantprotein therapeutics include economies of scale, continuous processing,and process simplification. (Warikoo et al., Integrated continuousproduction of recombinant therapeutic proteins, Biotechnol. Bioeng.109:3018-3029 (2012)). In addition, a key factor in reducing cost isincreasing the cellular productivity. Significant progress has been madein improving cellular productivity including improvements to expressionvectors, cell line engineering, medium development, and as well as otherfactors. (Dickson, A. J., Cell Line Development, Cell Line Dev. 6:83-96(2009)).

As higher levels of protein expression in cells are achieved, increasingamounts of cellular machinery are utilized for recombinant proteinexpression. In microbial systems, the metabolic burden of recombinantprotein expression has been shown to slow growth and reduce biomassaccumulation. (Wu et al., Metabolic Burden: Cornerstones in SyntheticBiology and Metabolic Engineering Applications, Trends Biotechnol.34:652-664 (2016)). Depending on the specific expression system, thisreduced growth rate and biomass accumulation can be attributed toreduced RNA synthesis, ribosome synthesis, translation initiation,translation elongation, or other factors. (See, e.g., Eames, M.,Kortemme, T., Cost-Benefit Tradeoffs in Engineered lac operons, Science336(6083):911-915 (2012); Kafri et al., The Cost of Protein Production,Cell Rep. 14:22-31 (2016); Scott et al., Interdependence of cell growthand gene expression: origins and consequences, Science330(6007):1099-1102 (2010)).

Different mammalian cell lines have been used for recombinant proteinproduction, including various lines of Chinese Hamster Ovary (CHO)cells. (See, e.g., Hu et al., Overexpressing Cyclin D1 in a EukaryoticCell line, U.S. Pat. No. 6,210,924; Goepfert et al., Protein Expressionfrom Multiple Nucleic Acids, U.S. Pat. No. 8,771,988; and Wurm, F. M.,CHO quasispecies—Implications for Manufacturing Processes, Processes1:296-311; doi:10.3390/pr1030296 (2013)).

In mammalian cells, there tends to be a modest correlation betweenrecombinant protein expression and growth rate indicating that metabolicburden also plays a role in limiting cellular productivity in mammalianexpression systems. (Chusainow et al., A study of monoclonalantibody-producing CHO cell lines: What makes a stable high producer?Biotechnol. Bioeng. 102:1182-1196 (2009); Jiang et al., Regulation ofrecombinant monoclonal antibody production in chinese hamster ovarycells: a comparative study of gene copy number, mRNA level, and proteinexpression, Biotechnol. Prog. 22:313-318 (2006); Pilbrough, W. et al.,Intraclonal protein expression heterogeneity in recombinant CHO cells,PLoS One 4 doi.org/10.1371/journal.pone.0008432 (2009); Wurm, F. M.,Production of recombinant protein therapeutics in cultivated mammaliancells, Nat. Biotechnol. 22:1393-1398 (2004)).

Kallehauge et al. showed that reducing expression of a selectable markerusing RNAi resulted in increased growth rate. (Kallehauge et al.,Ribosome profiling-guided depletion of an mRNA increases cell growthrate and protein secretion, Sci. Rep. 7:40388 (2017)).

Promoters combining enhancer and promoter elements from differentgenetic sources have been used to enhance recombinant expression in avariety of host cells. (E.g., Harvey, Hybrid promoters, WO 2008/020960A1; US 2008/12492 A1).

Previous studies have shown that the human CMV promoter and murine CMVpromoter can drive high level expression of heterologous expression inmammalian cells. (Mizushima & Nagata, pEF-BOS, a powerful mammalianexpression vector. Nucl. Acids Res., 18(17):5322 (1990); Masayuki &Tanaka, The CMV Enhancer Stimulates Expression of Foreign Genes from theHuman EF-1a Promoter, Analytical Biochemistry 247:179-181 (1997);Chattellard, P. et al., The Lupac bifunctional marker and its use inprotein production, WO 2006/058900 A1; Chattellard, P. et al.,Expression vectors comprising the mCMV 1E2 promoter, U.S. Pat. No.7,824,907; Hjelmstrom et al., Single IFN-beta fused to a mutated IgG Fcfragment, WO 2009/053368 A1; Gaucher et al., Cell line having a hightranscription activity for the production of proteins, in particulartherapeutic proteins, WO 2008/096070 A2; Flannery et al., Recombinantlubricin molecules and uses thereof, U.S. Pat. No. 7,642,236; Mosyak etal., Method for identifying or designing a candidate agent thatinteracts with LINGO-1 polypeptide using a LINGO-1 three-dimensionalstructure, U.S. Pat. No. 7,693,698; Mosyak et al., WO 2007/092370 A1).

Addition of introns also can increase expression of heterologousproteins (Lacy-Hulbert, A. et al., Interruption of coding sequences byheterologous introns can enhance the functional expression ofrecombinant genes, Gene Ther. 8(8):649-653 (2001); Brinster, R. L., etal., Introns increase transcriptional efficiency in transgenic mice,Proc. Natl. Acad. Sci. USA 85: 836-40 (1988)). The human and hamsterEF-1alpha promoter and introns have been shown to efficiently promotegene expression (Mizushima & Nagata, pEF-BOS, a powerful mammalianexpression vector, Nucl. Acids Res. 18(17):5322 (1990); Running Deer,J., & Allison, D. S., High-level expression of proteins in mammaliancells using Transcription Regulatory sequences from Chinese HamsterOvary EF-1alpha Gene, Biotechnology Progress 20:880-889 (2004); Allison,D. S., Recombinant method for making multimeric proteins, WO 2006/063292A1; Orlova et al., Improved elongation factor-1alpha-based vectors forstable high-level expression of heterologous proteins in Chinese hamsterovary cells, BMC Biotechnology 14:56 (2014)).

Combinations of human or murine CMV promoters combined with humanEF-1alpha introns showed a significant improvement over expressionconstructs with no intron (Kim, S.-Y. et al., The human elongationfactor 1 alpha (EF-1alpha) first intron highly enhances expression offoreign genes from the murine cytomegalovirus promoter, J. Biotechnol.93(2):183-87 (2002)).

Inducible expression systems have been used in mammalian and microbialcells to control expression levels of recombinant proteins. In order tomitigate the metabolic burden of protein expression during cell growthand to avoid potential toxicity of recombinant proteins in microbialexpression systems, an inducible expression system separating growth andrecombinant product expression phases is frequently used. This limitsthe impact of metabolic burden to only the production phase of theculture, when cell growth is not necessarily desirable. (See, e.g.,(see, Bentley, W. et al., Plasmid encoded protein: the principal factorin the “metabolic burden” associated with recombinant bacteria,Biotechnology and Bioengineering, Vol. 102, No. 5, 1283-07 (2009);Miroux, B et al., Over-production of proteins in Escherichia coli mutanthosts that allow synthesis of some membrane proteins and globularproteins at high levels, J. Mol. Biol. 260:289-298 (1996); Rosano, G Land Ceccarelli, E A, Recombinant protein expression in Escherichia coli:Advances and challenges, Front. Microbiol. 5(Art. 172):1-17 (2014)).

In contrast, for isolation of mammalian cell lines suited for industrialproduction of proteins, constitutive expression vectors are typicallyemployed. Inducible systems are typically utilized for only thoseproteins that are toxic when over expressed.

There are several reports that expression of toxic proteins in mammaliansystems leads to slower growth or cell line instability. (Umana, P. etal., Tetracycline-regulated overexpression of glycosyltransferases inChinese hamster ovary cells, Biotechnol. Bioeng. 65(5):542-549 (1999);Misaghi, S. et al., It's time to regulate: Coping with product-inducednongenetic clonal instability in CHO cell lines via regulated proteinexpression, Biotechnol Prog. 2014; 30(6):1432-1440 (2014); Jones, J. etal., Optimization of tetracycline-responsive recombinant proteinproduction and effect on cell growth and ER stress in mammalian cells,Biotechnol Bioeng. 91(6):722-732 (2005)). For example, Misaghi et al.(2014), supra, showed that using a regulated expression system thatrestricts expression of moderately toxic antibody during cell linedevelopment allowed isolation of stable cell lines, whereas constitutiveexpression of this protein yielded unstable cell lines, consistent withthe idea that the metabolic burden of a toxic protein can result in theenrichment of clones with reduced protein expression. Similarly,regulated expression of the moderately toxic protein transferrin showedthat clones isolated in the repressed state expressed at higher levelscompared to clones where transferrin was constitutively expressed (Joneset al. (2005), supra).

Using a cumate-regulated system, Poulain et al. showed an increase inexpression of an Fc fusion protein, as well as an antibody, when cellswere selected in the absence of expression, when compared to twoconstitutive promoters. In this case, neither the Fc fusion protein northe antibody displayed obvious toxicity. (Poulain, A. et al., Rapidprotein production from stable CHO cell pools using plasmid vector andthe cumate gene-switch, J Biotechnol. 255:16-27 (2017)).

Using a doxycycline-inducible system, Li et al. observed fewer numbersof clones when cells were selected in presence of protein expressionthan when compared with non-induced cultures. This observation is alsoconsistent with the hypothesis of metabolic burden impacting growth oftransfected cells. (Li, Z et al., Simple piggyBac transposon-basedmammalian cell expression system for inducible protein production, ProcNatl Acad Sci USA. 110(13):5004-5009 (2013)).

The Tet repressor (TetR), which is encoded by the bacterial transposon,Tn10, has been used to regulate inducible gene expression in mammaliancells. TetR binds to a DNA sequence (TetO) in the absence oftetracycline. Upon binding to tetracycline, TetR undergoes aconformational change that abrogates the binding of TetR to TetO. Yao etal. had shown that the human CMV enhancer promoter could be regulated bytetracycline by incorporating a TetO sequence between the TATA box andthe transcriptional start site (TSS). (See, Yao et al., Tetracyclinerepressor, tetR, rather than the tetR-mammalian cell transcriptionfactor fusion derivatives, regulates inducible gene expression inmammalian cells, Hum. Gene Ther. 9(13):1939-50 (1998); Yao et al. U.S.Pat. No. 5,972,650; Yao et al., WO99/00510).

There is a need for enhanced recombinant expression of proteins bymammalian cells in large batch or continuous culture to support robustproduction of biologics in a variety of mammalian cell lines, and thereis a need for improved methods of selecting stable mammalian cells linesthat can deliver enhanced expression. The present invention providesthese.

SUMMARY OF THE INVENTION

The present invention relates to a recombinant expression vector forstable expression of one or more proteins of interest in mammalian hostcells, by promoting genomic integration of the expression cassettesincluded in the vector, by virtue of the 5′ and 3′ PiggyBac transposonITRs the vector comprises. In one embodiment, the recombinant expressionvector of the invention includes:

(a) a 5′ PiggyBac ITR comprising the nucleotide sequence of SEQ IDNO:45;(b) a first expression cassette, comprising:

-   -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding an protein of interest        operably linked to the control sequence; and    -   (iii) a polyadenylation site operably linked 3′ to the open        reading frame;        (c) a second expression cassette, comprising:    -   (i) a weak constitutive promoter, operably linked to an open        reading frame encoding a selectable marker; and    -   (ii) a polyadenylation site operably linked 3′ to the open        reading frame; and        (d) a 3′ PiggyBac ITR comprising the nucleotide sequence of SEQ        ID NO:47.

The inventive combination of a mCMV enhancer sequence with a ratEF-1alpha intron sequence in the hybrid promoter facilitates recombinantexpression of proteins of interest, particularly by CHO cells, with hightiters and high specific productivity suitable for industrial productionof biologic molecules, such as, but not limited to, an antigen bindingprotein, an immunoglobulin, an antibody or antibody fragment, or hormone(e.g., as human therapeutics to prevent or treat disease).

In other embodiments, the recombinant expression vector of the inventionallows stable inducible expression of the one or more proteins ofinterest in mammalian host cells, by virtue of one or more TetOsequences in a control sequence of an expression cassette, while thevector promotes genomic integration of the expression cassettes includedin the vector, by virtue of the 5′ and 3′ PiggyBac transposon ITRs thevector comprises. In particular, the recombinant expression vector,comprises:

(a) a 5′ PiggyBac ITR comprising the nucleotide sequence of SEQ IDNO:45;(b) a first expression cassette, comprising:

-   -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence, comprising one or more TetO sequences inserted            within the CMV promoter sequence of the first promoter;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding a protein of interest        operably linked to the control sequence; and    -   (iii) a polyadenylation site operably linked 3′ to the open        reading frame;        (c) a second expression cassette, comprising:    -   (i) a weak constitutive promoter, operably linked to an open        reading frame encoding a selectable marker; and    -   (ii) a polyadenylation site operably linked 3′ to the open        reading frame; and        (d) a 3′ PiggyBac ITR comprising the nucleotide sequence of SEQ        ID NO:47. An example of such a vector is pJVec_5 (see, FIG. 28),        further described herein.

This recombinant expression vector, allowing inducible expression of theprotein of interest in a mammalian host cell, stably transfectedtherewith, is useful, inter alia, for a method of selecting a stableproduction cell line for manufacturing the protein of interest. Theinventive method comprises the following steps:

(a) culturing a mammalian host cell stably transfected with therecombinant expression vector described in the paragraph above (whichcomprises the one or more TetO sequences in a control sequence of anexpression cassette), under selective pressure with respect to aselectable marker constitutively expressed from the weak constitutivepromoter, in an aqueous medium under physiological conditions, whereinthe mammalian host cell is capable of expressing TetR, in the absence oftetracycline or a tetracycline analog in the medium, whereby expressionof protein from the first expression cassette is repressed;(b) selecting a viable cell line from the host cell(s) cultured in step(a);(c) culturing the viable cell line from step (b) in an aqueous mediumcontaining tetracycline or a tetracycline analog in an amount sufficientto bind TetR in the host cell(s), whereby expression of the protein ofinterest by the host cell is derepressed; and(d) detecting the protein of interest in the culture medium;(e) selecting a stable production cell line from step (c) that producesa greater amount of the protein of interest relative to a controltransfectant in which the aqueous medium in steps (a) and (c) containedtetracycline or a tetracycline analog in an amount sufficient to bindTetR in the host cell, whereby the expression of the protein of interestwas derepressed in the control transfectant.

In another aspect, the invention is directed to a recombinant expressionvector that is particularly useful for expression of immunoglobulins,e.g., antibodies, and to a mammalian host cell (e.g., a CHO cell)containing the vector. In some embodiments, the recombinant expressionvector includes:

(a) a first expression cassette, comprising:

-   -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding a first immunoglobulin        subunit operably linked to the control sequence; and    -   (iii) a first polyadenylation site operably linked 3′ to the        open reading frame;        (b) a second expression cassette 3′ to the first expression        cassette, comprising:    -   (i) a control sequence comprising a promoter;    -   (ii) an open reading frame encoding a second immunoglobulin        subunit operably linked to the promoter; and    -   (iii) a second polyadenylation site operably linked 3′ to the        open reading frame; and        (c) a transcription termination sequence 3′ to the first        expression cassette and 5′ to the second expression cassette.

Other embodiments of the recombinant (expression vector of the inventionallow inducible expression of the one or more proteins of interest inmammalian host cells, by virtue of one or more TetO sequences in acontrol sequence of an expression cassette. These embodiments of therecombinant expression vector include:

(a) a first expression cassette, comprising:

-   -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence, comprising one or more TetO sequences inserted            within the CMV-P sequence;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding a first immunoglobulin        subunit operably linked to the control sequence; and    -   (iii) a first polyadenylation site operably linked 3′ to the        open reading frame;        (b) a second expression cassette 3′ to the first expression        cassette, comprising:    -   (i) a control sequence comprising a promoter;    -   (ii) an open reading frame encoding a second immunoglobulin        subunit operably linked to the promoter; and    -   (iii) a second polyadenylation site operably linked 3′ to the        open reading frame; and        (c) a transcription termination sequence 3′ to the first        expression cassette and 5′ to the second expression cassette.

The present invention also relates to mammalian host cell (e.g., a CHOcell) containing any of the inventive recombinant expression vector(s)and a method of producing a protein of interest, in vitro, that involvesculturing the mammalian host cell containing the inventive expressionvector, in an aqueous medium under physiological conditions permittingexpression of the protein of interest; and recovering the protein ofinterest from the medium.

The foregoing summary is not intended to define every aspect of theinvention, and additional aspects are described in other sections, suchas the Detailed Description of Embodiments. The entire document isintended to be related as a unified disclosure, and it should beunderstood that all combinations of features described herein arecontemplated, even if the combination of features are not found togetherin the same sentence, or paragraph, or section of this document.

In addition to the foregoing, the invention includes, as an additionalaspect, all embodiments of the invention narrower in scope in any waythan the variations defined by specific paragraphs above. For example,certain aspects of the invention that are described as a genus, and itshould be understood that every member of a genus is, individually, anaspect of the invention. Also, aspects described as a genus or selectinga member of a genus, should be understood to embrace combinations of twoor more members of the genus. Although the applicant(s) invented thefull scope of the invention described herein, the applicants do notintend to claim subject matter described in the prior art work ofothers. Therefore, in the event that statutory prior art within thescope of a claim is brought to the attention of the applicants by aPatent Office or other entity or individual, the applicant(s) reservethe right to exercise amendment rights under applicable patent laws toredefine the subject matter of such a claim to specifically exclude suchstatutory prior art or obvious variations of statutory prior art fromthe scope of such a claim. Variations of the invention defined by suchamended claims also are intended as aspects of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows schematic maps of some exemplary expression constructs.

FIG. 2 shows a schematic map of exemplary Vector D.

FIGS. 3A and 3B shows DXB11 cell produced Fc-A protein titer (FIG. 3A)and specific productivity (FIG. 3B) in ProCHO™ 4 culture mediumcontaining 150 nM methotrexate (MTX) on Day 8. Each error bar isconstructed using 1 standard error of the mean.

FIGS. 4A and 4B shows DXB11 cell produced Fc-A protein titer (FIG. 4A)and specific productivity (FIG. 4B) in PowerCHO™ 2 medium at 500 nM MTXon Day 8. Each error bar is constructed using 1 standard error of themean.

FIGS. 5A and 5B shows Fc-A protein titer (FIG. 5A) and specificproductivity (FIG. 5B) for DG44 in PowerCHO™ 2 medium at 1 μM MTX andDXB11 in Excell302 medium at 500 nM MTX, on Day 10. Each error bar isconstructed using 1 standard error of the mean.

FIG. 6 shows a schematic map of pJV56 with the inventive mCMVenhancer/rEF-1α intron hybrid promoter driving LacZ expression.

FIG. 7 shows a schematic map of pJV57, which was the same as pJV56,except that part of the mCMV promoter (mCMV-P) was replaced with humanCMV promoter (hCMV-P) and TetO sequences.

FIG. 8 shows a schematic map of pJV59, which was the same as pJV56, butwith an optimized human CMV promoter ((hCMV-P); after Patwardhan et al.,“High-resolution analysis of DNA regulatory elements by syntheticsaturation mutagenesis”, Nature Biotechnology 27(12):1173-75 (2009)),substituted for part of the mCMV promoter (mCMV-P) sequence.

FIG. 9 shows a schematic map of pJV60, which was the same as pJV57,except for changes to the TetO sequences (maintaining TetR binding) tomatch the optimized human CMV promoter (hCMV-P) sequence.

FIG. 10 shows a schematic representation of the human CMV promoter-Tetoperator (TetO; “Tet”) inserted into the mCMV promoter (“mCMVP”)sequence, 3′ to the mCMV enhancer element (“MCVE”) sequence. Thisinsertion replaced part of the mCMV promoter with a hCMV promoter(hCMVP) sequence. The relative position of the first leader sequence isalso represented by “TPL.”

FIG. 11 shows a schematic comparison of the DNA sequences of a segmentof pJV56 (SEQ ID NO:16) and a segment of pJV57 (SEQ ID NO:15). Thesegment of pJV57 shown in SEQ ID NO:15 includes a segment (SEQ ID NO:9)that incorporates a partial hCMV promoter sequence (SEQ ID NO:24) and,3′ to SEQ ID NO:24, a TetO sequence (SEQ ID NO:23, which contains asmaller TetO sequence SEQ ID NO:29). Arrows shown in the TetO sequence(SEQ ID NO:29) indicate palindromic TetR binding sites. The mCMVpromoter (mCMV-P) sequence and hCMV promoter (hCMV-P) sequence are thosesequences from the TATA box through the start site of transcription. SEQID NO:25 is the 3′ end of a mCMV-P sequence found in both pJV57 andpJV56, and in pJV57 is found 3′ to SEQ ID NO:9. The transcription startis the guanine residue in the 3′ subsequence taccg of SEQ ID NO:25. Notethat the inserted TetO sequence (SEQ ID NO:23) most certainly impactsthe transcription start site, since the transcription start site istypically ˜30 bases 3′ to the 5′ T of the TATA box. The relativeposition of the first leader sequence is also represented by “TPL,” andsome nucleotide residues at the 5′ end of the TPL are shown.

FIG. 12 shows a schematic comparison of segments of the DNA sequences ofpJV57 and pJV60. In the segment shown of pJV60 (SEQ ID NO:18), the TetOsequences in the corresponding segment of pJV57 (SEQ ID NO:17) werechanged to match the sequences that increased expression surrounding thetranscription start site in the study by Patwardhan et al.,“High-resolution analysis of DNA regulatory elements by syntheticsaturation mutagenesis”, Nature Biotechnology 27(12):1173-75 (2009).

FIG. 13 shows a schematic comparison of segments of the DNA sequences ofpJV56 and pJV59. In this segment of pJV59 (SEQ ID NO:20), optimized hCMVpromoter sequences in the corresponding sequence of pJV56 (SEQ ID NO:19)replaced part of the mCMV promoter (mCMV-P) sequence in a variation ofthe mCMV enhancer/rat EF-1a intron hybrid promoter of the invention.

FIG. 14 shows regulation of specific β-galactosidase expression for eachof the indicated vectors. T-REx™-CHO cells expressing TetR weretransiently transfected with pJV56, pJV57, pJV59, pJV60, or the controlplasmid pcDNA5/TO/LacZ. Cell were incubated for 24 hours and thentreated with tetracycline (Tet) or left untreated for 24 hours. Cellswere lysed and LacZ was analyzed enzymatically. The fold-differencebetween the (+Tet) compared to (−Tet) is shown above the bars, exceptfor the positive control (pcDNA5/TO/LacZ).

FIG. 15 shows a schematic map of pJV40, including an open reading framefor TetR.

FIG. 16 illustrates expression of LacZ (beta-galactosidase protein) byCHO-K1/TetR cells (clone 3E7) expressing TetR, which were transientlytransfected with pJV56, pJV57, pJV59, pJV60, or the control plasmidpcDNA5/TO/LacZ. Cell were incubated for 24 hours and then treated withtetracycline (Tet) or left untreated for 24 hours. Cells were lysed andLacZ was analyzed enzymatically. The fold-difference between the (+Tet)compared to (−Tet) is shown above the bars.

FIG. 17 illustrates expression of LacZ (beta-galactosidase protein) byCHO-K1/TetR cells (clone 3F9) expressing TetR, which were transientlytransfected with pJV56, pJV57, pJV59, pJV60, or the control plasmidpcDNA5/TO/LacZ. Cell were incubated for 24 hours and then treated withtetracycline (Tet) or left untreated for 24 hours. Cells were lysed andLacZ was analyzed enzymatically. The fold-difference between the (+Tet)compared to (−Tet) is shown above the bars.

FIG. 18 illustrates expression of LacZ (beta-galactosidase protein) byCHO-K1/TetR cells (clone 4G2) expressing TetR, which were transientlytransfected with pJV56, pJV57, pJV59, pJV60, or the control plasmidpcDNA5/TO/LacZ. Cell were incubated for 24 hours and then treated withtetracycline (Tet) or left untreated for 24 hours. Cells were lysed andLacZ was analyzed enzymatically. The fold-difference between the (+Tet)compared to (−Tet) is shown above the bars.

FIG. 19A-C show that an inducible transposon expression system canregulate cellular growth in CHOK1-TetR (GS KO) pools expressing anFc-fusion protein during growth phase. FIG. 19A shows a schematicrepresentation of vectors pJVEC_2 and pJVec_3 when integrated into thegenome to stably transfect TetR-GS KO cells. GS=glutamine synthetase;CP=constitutive promoter; mCMV=mouse cytomegalovirus promoter;TPL=tripartite leader sequence; rEF-1a: =rat EF-1a intron;Fc-A=recombinant Fc-fusion protein; pA=polyA; TetO=Tet-operatorsequence. FIG. 19B shows growth profiles, and FIG. 19C shows viabilityover the first 3 weeks of selection in cell culture medium containing 75mM L-methionine sulfoximine (MSX). Circles are cultures without thetetracycline analog, doxycycline (−Dox), and star symbols are cultureswith doxycycline (+Dox). Each trace represents a transfection replicate.n=4.

FIG. 20A-B show that an inducible transposon expression system canregulate productivity in CHOK1-TetR (GS KO) pools expressing anFc-fusion protein during production. FIG. 20A shows Day 10 titers ofproduction cultures in CD OptiCHO™ medium. (−) denotes pools that didnot receive doxycycline (Dox) during selection. FIG. 20B shows viablecell density (VCD) and average viability over time. Circles are cultureswithout Dox and star symbols are cultures with Dox. Each tracerepresents a transfection replicate. n=4.

FIG. 20C shows a linear correlation between specific productivity (qP)and Fc-A mRNA levels during fed-batch production. n=4-8, for twoindependent experiments. pJVec3 had Dox during selection and production.pJVec3(−) transfected pools were selected in the absence of Dox.Cultures of pJVec3(−) were treated with Dox during production and areindicated by the x symbols in the dashed oval.

FIG. 21A shows a schematic representation of the vector map ofinducible, pJVec_4, when integrated into the genome. FIG. 21B showstiter and qP of pools on day 10 of fed-batch cultures in CD OptiCHO™medium. n=4. FIG. 21C shows a correlation between protein production(qP) and mAb light chain (LC) and heavy chain (HC) mRNA levels duringfed-batch production. Data represented by “+” symbols are +Dox; andcircles represent −Dox. FIG. 21D shows LC/HC ratios for −Dox and +Doxconditions, respectively.

FIG. 22A-B illustrates expression vector pJVec_5 and expression bytransfected CHO cells. FIG. 22A shows a schematic representation of thevector map of pJVec_5, when integrated into the genome. FIG. 22B showsselection curves of transfected pools in CD OptiCHO™ medium −glutamine(−Q) and +/−Dox. n=3 each. Circles represent data points for cultureswithout Dox, and “+” symbols represent data points for cultures withDox.

FIG. 23A-C shows results from an experiment. FIG. 23A shows Day 10titers/qP from a fed-batch protein production in a chemically definedculture medium without growth factors or other proteins, with Hyclonefeeds A/B. n=3. FIG. 23B shows growth curves with Dox added duringproduction. FIG. 23C shows growth curves of cultures in which Dox wasnot added during production. (−) denotes pools that did not receive Doxduring selection.

FIG. 24A-B show qPCR analysis (FIG. 24A) of mAb_A LC and HC expressionduring production. n=3, Data shown are representative of 2 independentexperiments. FIG. 24B shows the LC/HC ratio.

FIG. 25A shows a schematic representation of pJVec_1 (inducible) andcontrol (constitutive).

FIG. 25B shows results of expression of an Fc-fusion protein transientlytransfected into Clone_A cells. n=2

FIG. 26 shows recovery curves of Clone 9G1 pools transfected withpJVec_2 or pJVec_3 selected in CD OptiCHO medium minus glutamine (−Q),with (*) or without (O) +Dox at 75 or 100 μM L-methionine sulfoximine(MSX).

FIG. 27A shows Day 10 titers/qP from a fed-batch production in achemically defined culture medium without growth factors or otherproteins, with Hyclone feeds A/B. n=3, and FIG. 27B shows representativegrowth curves during production.

FIG. 28 shows a schematic representation of the vector map of inducible,pJVec_5.

DETAILED DESCRIPTION OF EMBODIMENTS

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the subject matter described.

Definitions

Unless otherwise defined herein, scientific and technical terms used inconnection with the present application shall have the meanings that arecommonly understood by those of ordinary skill in the art. Further,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. Thus, as usedin this specification and the appended claims, the singular forms “a”,“an” and “the” include plural referents unless the context clearlyindicates otherwise. For example, reference to “a protein” includes aplurality of proteins; reference to “a cell” includes populations of aplurality of cells.

In some embodiments, the present invention relates to a recombinantPiggyBac transposon-based vector for stable expression of one or moreproteins of interest in mammalian host cells. The PiggyBac (PB)transposon is a mobile genetic element that efficiently transposesbetween vectors and host cell chromosomes via a “cut and paste”transposition mechanism. During transposition, the PB transposaserecognizes transposon-specific inverted terminal repeat sequences (ITRs)located on both the 5′ and 3′ ends of the transposon-based vector andmoves the vector contents between the 5′ and 3′ ITRs from the originalvector sites and integrates them into TTAA chromosomal sites. Forpurposes of the invention the “5′ PiggyBac ITR” comprises the nucleotidesequence of SEQ ID NO:45:CCCTAGAAAGATAGTCTGCGTAAAATTGACGCATGCATTCTTGAAATATTGCTCTCTCTTTCTAAATAGCGCGAATCCGTCGCTGTGCATTTAGGACATCTCAGTCGCCGCTTGGAGCTCCCGTGAGGCGTGCTTGTCAATGCGGTAAGTGTCACTGATTTTGAACTATAACGACCGCGTGAGTCAAAATGACGCATGATTATCTTTTACGTGACTTTTAAGATTTAACTCATACGATAATTATATTGTTATTTCATGTTCTACTTACGTGATAACTTATTATATATATATTTTCTTGTTATAGATATC//SEQ ID NO:45. For purposes of theinvention “3′ PiggyBac ITR” comprises the nucleotide sequence of SEQ IDNO:47:

SEQ ID NO: 47 GATAAAAGTTTTGTTACTTTATAGAAGA AATTTTGAGTTTTTGTTTTTTTTAATAAATAAATAAACATAAATAAATTGTTTGTT GAATTTATTATTAGTATGTAAGTGTAAATATAATAAAACTTAATATCTATTCAAA TTAATAAATAAACCTCGATATACAGACCGATAAAACACATGCGTCAATTTTACAC ATGATTATCTTTAACGTACGTCACAATATGATTATCTTTCTAGGG//.

The present invention relates to a hybrid promoter for regulatingrecombinant expression of one or more proteins of interest. Theinventive promoter includes a mCMV enhancer sequence operably linked toa rat EF-1alpha intron sequence. The term “mCMV,” used interchangeablywith “muCMV,” refers to murine cytomegalovirus, which is a herpesvirusof the subfamily betaherpesviridae. The mCMV is a double-strandedenveloped DNA virus with host specificity for mice. Similarly, the term“hCMV,” or interchangeably “huCMV,” refers to human cytomegalovirus.

The “mCMV enhancer sequence,” with respect to the present invention,includes:

-   -   (i) a mCMV enhancer element (“mCMV-E”); and, at the 3′ end of        the mCMV enhancer sequence,    -   (ii) a CMV promoter sequence (“CMV-P”; i.e., a nucleotide        sequence segment beginning at, and including, the TATA box        through the start site of transcription); the CMV promoter        sequence can be derived from mCMV, hCMV, simian CMV, rat CMV, or        any other variety of CMV, or it can be an optimized version of a        CMV-P, which is functional to enable transcription in mammalian        cells, such as CHO cells.

The term “recombinant” indicates that the material (e.g., a nucleic acidor a polypeptide) has been artificially or synthetically (i.e.,non-naturally) altered by human intervention. The alteration can beperformed on the material within, or removed from, its naturalenvironment or state. For example, a “recombinant nucleic acid” is onethat is made by recombining nucleic acids, e.g., during cloning, DNAshuffling or other well known molecular biological procedures. Examplesof such molecular biological procedures are found in Maniatis et al.,Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y. (1982). A “recombinant DNA molecule,” iscomprised of segments of DNA joined together by means of such molecularbiological techniques. The term “recombinant protein” or “recombinantpolypeptide” as used herein refers to a protein molecule which isexpressed using a recombinant DNA molecule. A “recombinant host cell” isa cell that contains and/or expresses a recombinant nucleic acid.

The term “naturally occurring” as used throughout the specification inconnection with biological materials such as polypeptides, nucleicacids, host cells, and the like, refers to materials which are found innature.

The term “control sequence” or “control signal” refers to apolynucleotide sequence that can, in a particular host cell, affect theexpression and processing of coding sequences to which it is ligated.The nature of such control sequences may depend upon the host organism.In particular embodiments, control sequences for prokaryotes may includea promoter, a ribosomal binding site, and a transcription terminationsequence. Control sequences for eukaryotes, including mammalian cells,can include promoters comprising one or a plurality of recognition sitesfor transcription factors, transcription enhancer sequences or elements,intron sequences, polyadenylation sites, and transcription terminationsequences. Control sequences can include leader sequences and/or fusionpartner sequences. Promoters and enhancers consist of short arrays ofDNA that interact specifically with cellular proteins involved intranscription (Maniatis, et al., Science 236:1237 (1987)). Promoter andenhancer elements have been isolated from a variety of eukaryoticsources including genes in yeast, insect and mammalian cells and viruses(analogous control elements, i.e., promoters, are also found inprokaryotes). The selection of a particular promoter and enhancerdepends on what cell type is to be used to express the protein ofinterest. Some eukaryotic promoters and enhancers have a broad hostrange while others are functional in a limited subset of cell types (forreview see Voss, et al., Trends Biochem. Sci., 11:287 (1986) andManiatis, et al., Science 236:1237 (1987)).

A “promoter” is a region of DNA including a site at which RNA polymerasebinds to initiate transcription of messenger RNA by one or moredownstream structural genes. Promoters are located near thetranscription start sites of genes, on the same strand and upstream onthe DNA (towards the 5′ region of the sense strand). Promoters aretypically about 100-1000 bp in length. A common feature of promoterregions in eukaryotes is the TATA box, it is found about 25 basesupstream from the transcription start site and has the ideal sequence ofTATAAAT. The closeness of the actual sequence to this ideal sequenceeffects the ability of the RNA polymerase complex to bind to the DNA andhence initiate the transcription process.

In some embodiments, the inventive recombinant expression vectorincludes an expression cassette comprising a weak constitutive promoter,operably linked to an open reading frame encoding a selectable marker. A“constitutive promoter” is: (1) a promoter sequence that initiates mRNAsynthesis independent of the influence of regulation, or (2) a promotersequence that initiates mRNA synthesis independent, or substantiallyindependent, of the influence of regulation, under physiologicalconditions normally associated with cell culture for the expression of aprotein of interest in an industrial protein manufacturing setting. Thespecific nucleic acid (i.e., nucleotide) sequence of the promoterdetermines the strength of the promoter (a strong promoter leads to arelatively high rate of transcription initiation). Commonly usedconstitutive promoters for mammalian cell systems include simian virus40 early promoter (SV40), cytomegalovirus immediate-early promoter(CMV), human Ubiquitin C promoter (UBC), human elongation factor 1apromoter (EF1A), mouse phosphoglycerate kinase 1 promoter (PGK), andchicken β-Actin promoter coupled with CMV early enhancer (CAGG). A “weakconstitutive promoter” is a constitutive promoter that will not initiatetranscription as efficiently as a strong promoter, for example, amodified version of one of the foregoing list of constitutive promoters.Thus, an example of a weak constitutive promoter is a deleted SV40promoter. (See, e.g., Hartman et al., Vectors and host cells comprisinga modified SV40 promoter for protein expression, U.S. Ser. No.10/053,720; and Hartman et al., DAC HYP compositions and methods, U.S.Pat. No. 9,260,528B2). Another useful example of a weak constitutivepromoter for purposes of the present invention is the PGK promoterdescribed in Qin J Y et al. (Qin, J Y, Zhang L, Clift K L, Hulur I,Xiang A P, Ren B-Z, et al. (2010), Systematic Comparison of ConstitutivePromoters and the Doxycycline-Inducible Promoter. PLoS ONE 5(5): e10611.doi.org/10.1371/journal.pone.0010611; see, also, e.g., Li, J. & Zhang,Y., Relationship between promoter sequence and its strength in geneexpression, Eur. Phys. J. E 37: 86 (2014)). One particularly usefulexample of a weak constitutive promoter for purposes of the presentinvention is a deleted SV40 promoter comprising the nucleotide sequenceof SEQ ID NO:46:

SEQ ID NO: 46 TCCCGCCCCTAACTCCGCCCAGTTCCGC CCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCG CCTCGGCCTCTGAGCTATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGG CTTTTGCAAAAAGCT//.The deleted SV40 promoter comprising the nucleotide sequence of SEQ IDNO:46 is used, e.g., in vector pJVec_5 (see, FIG. 28). Another usefulexample is a further truncation of the SV40 promoter that furtherweakens the promoter, e.g., a deleted SV40 promoter comprising thenucleotide sequence of SEQ ID NO:53:GTTCCGCCCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCGGCCTCTGAGCTATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAAAAGCT//SEQ ID NO:53. The weak constitutive promoter isoperably linked to an open reading frame encoding a selectable marker,which selectable marker confers upon cells transfected with anexpression vector, as described herein, a trait or characteristic thatbe used to identify transfected cells from non-transfected cells. Usefulselectable markers and there coding sequences are well known in the art.They can confer traits such as, but not limited to, resistance to atoxin, heavy metal, antibiotic, or other agent, prototrophy in anauxotrophic host, the ability to grow in a medium free of an essentialnutrient, the ability to synthesize an essential metabolite. Selectablemarkers commonly used in transfecting mammalian cells, such as CHOcells, include, but are not limited to, glutamine synthetase (GS),puromycin resistance (PurR), neomycin resistance (NeoR), zeomycinresistance (ZeoR), or dihydrofolate reductase (DHFR). A useful exampleof a glutamine synthetase coding sequence has the nucleotide sequence ofSEQ ID NO:49, or a degenerate DNA sequence:

SEQ ID NO: 49 ATGGCCACCTCAGCAAGTTCCCACTTGAACAAAAACATCAAGCAAATGTACTTGTGCCTGCCCCAGGGTGAGAAAGTCCAAGCCATGTATATCTGGGTTGATGGTACTGGAGAAGGACTGCGCTGCAAAACCCGCACCCTGGACTGTGAGCCCAAGTGTGTAGAAGAGTTACCTGAGTGGAATTTTGATGGCTCTAGTACCTTTCAGTCTGAGGGCTCCAACAGTGACATGTATCTCAGCCCTGTTGCCATGTTTCGGGACCCCTTCCGCAGAGATCCCAACAAGCTGGTGTTCTGTGAAGTTTTCAAGTACAACCGGAAGCCTGCAGAGACCAATTTAAGGCACTCGTGTAAACGGATAATGGACATGGTGAGCAACCAGCACCCCTGGTTTGGAATGGAACAGGAGTATACTCTGATGGGAACAGATGGGCACCCTTTTGGTTGGCCTTCCAATGGCTTTCCTGGGCCCCAAGGTCCGTATTACTGTGGTGTGGGCGCAGACAAAGCCTATGGCAGGGATATCGTGGAGGCTCACTACCGCGCCTGCTTGTATGCTGGGGTCAAGATTACAGGAACAAATGCTGAGGTCATGCCTGCCCAGTGGGAATTTCAAATAGGACCCTGTGAAGGAATCCGCATGGGAGATCATCTCTGGGTGGCCCGTTTCATCTTGCATCGAGTATGTGAAGACTTTGGGGTAATAGCAACCTTTGACCCCAAGCCCATTCCTGGGAACTGGAATGGTGCAGGCTGCCATACCAACTTTAGCACCAAGGCCATGCGGGAGGAGAATGGTCTGAAGCACATCGAGGAGGCCATCGAGAAACTAAGCAAGCGGCACCGGTACCACATTCGAGCCTACGATCCCAAGGGGGGCCTGGACAATGCCCGTCGTCTGACTGGGTTCCACGAAACGTCCAACATCAACGACTTTTCTGCTGGTGTCGCCAATCGCAGTGCCAGCATCCGCATTCCCCGGACTGTCGGCCAGGAGAAGAAAGGTTACTTTGAAGACCGCCGCCCCTCTGCCAATTGTGACCCCTTTGCAGTGACAGAAGCCATCGTCCGCACATGCCTTCTCAATGAGACTGGCGACGA GCCCTTCCAATACAAAAACTAA//.

In general, an “enhancer” is a short (50-1500 bp) region of DNA that canbe bound with one or more activator proteins (transcription factors) toactivate transcription of a gene.

A mCMV enhancer sequence useful in the inventive hybrid promotercomprises a nucleotide sequence at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to the nucleotidesequence of SEQ ID NO:2, which contains a CMV promoter (CMV-P) sequenceat its 3′ end (bold underlined sequence in SEQ ID NO:2) beginning atnucleotide position 588 (including a TATA-box and transcriptional startsite, i.e., TATAAGAGG CGCGA C CAGCG TCGG TACCG//SEQ ID NO:28; boldunderlined in SEQ ID NO:2 below; SEQ ID NO:28 also comprises SEQ IDNO:26):

SEQ ID NO: 2 GTCAACAGGA AAGTTCCATT GGAGCCAAGT ACATTGAGTCAATAGGGACT TTCCAATGGG TTTTGCCCAG TACATAAGGTCAATGGGAGG TAAGCCAATG GGTTTTTCCC ATTACTGGCACGTATACTGA GTCATTAGGG ACTTTCCAAT GGGTTTTGCCCAGTACATAA GGTCAATAGG GGTGAATCAA CAGGAAAGTCCCATTGGAGC CAAGTACACT GAGTCAATAG GGACTTTCCATTGGGTTTTG CCCAGTACAA AAGGTCAATA GGGGGTGAGTCAATGGGTTT TTCCCATTAT TGGCACGTAC ATAAGGTCAATAGGGGTGAG TCATTGGGTT TTTCCAGCCA ATTTAATTAAAACGCCATGT ACTTTCCCAC CATTGACGTC AATGGGCTATTGAAACTAAT GCAACGTGAC CTTTAAACGG TACTTTCCCATAGCTGATTA ATGGGAAAGT ACCGTTCTCG AGCCAATACACGTCAATGGG AAGTGAAAGG GCAGCCAAAA CGTAACACCGCCCCGGTTTT CCCCTGGAAA TTCCATATTG GCACGCATTCTATTGGCTGA GCTGCGTTCT ACGTGGG TAT AAGAGGCGCG ACCAGCGTCG GTACCG //.

Another exemplary mCMV enhancer sequence useful in the inventive hybridpromoter comprises a nucleotide sequence at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% identical to thenucleotide sequence of SEQ ID NO:33, which contains a CMV promotersequence at its 3′ end (bold underlined sequence in SEQ ID NO:33)beginning at position 588, which includes a TATA-box and transcriptionalstart site, i.e.,TATATAAGCAGAGCTCGTTTAGTGAACCGTCAGTTCGTCTCTAGACGCCAACCG//SEQ ID NO:35;bold underlined sequence in SEQ ID NO:33 below; SEQ ID NO:35 alsocomprises SEQ ID NO:24):

SEQ ID NO: 33 GTCAACAGGAAAGTTCCATTGGAGCCAAGTACATTGAGTCAATAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATGGGAGGTAAGCCAATGGGTTTTTCCCATTACTGGCACGTATACTGAGTCATTAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATAGGGGTGAATCAACAGGAAAGTCCCATTGGAGCCAAGTACACTGAGTCAATAGGGACTTTCCATTGGGTTTTGCCCAGTACAAAAGGTCAATAGGGGGTGAGTCAATGGGTTTTTCCCATTATTGGCACGTACATAAGGTCAATAGGGGTGAGTCATTGGGTTTTTCCAGCCAATTTAATTAAAACGCCATGTACTTTCCCACCATTGACGTCAATGGGCTATTGAAACTAATGCAACGTGACCTTTAAACGGTACTTTCCCATAGCTGATTAATGGGAAAGTACCGTTCTCGAGCCAATACACGTCAATGGGAAGTGAAAGGGCAGCCAAAACGTAACACCGCCCCGGTTTTCCCCTGGAAATTCCATATTGGCACGCATT CTATTGGCTGAGCTGCGTTCTACGTGGGTATATAAGCAGAGCT CGTTTAGTGAACCGTCAGTTCGTCTCTAGACGCCAACCG //.

In some useful embodiments, in which tetracycline-inducible expressionis desired, the inventive hybrid promoter comprises one or more TetOsequences operably linked 3′ to the mCMV enhancer sequence, insertedwithin the CMV promoter (CMV-P) sequence at the 3′ end of the mCMVenhancer sequence. A “TetO” sequence means a nucleotide sequence, whichmaintains the ability to bind tetracycline repressor protein (TetR). TheTetO sequence is placed so that, in the presence of TetR protein, thereis binding of TetR to the TetO sequence, thereby disruptingtranscription to a detectable extent, compared to a control not havingTetO in the promoter driving transcription of a gene of interest, or toa control not having TetR. Examples of the TetO sequence include asequence having at least 95%, at least 96%, at least 97%, at least 98%,at least 99%, or 100% sequence identity to SEQ ID NO:29(TCCCTATCAGTGATAGAGATCTCCCTATCAGTGATAGAGA//SEQ ID NO:29) or having atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to SEQ ID NO:34(CTCCCTATCAGTGATCAGTTCCTCCCTATCAGTGATAGAGA//SEQ ID NO:34). In someuseful embodiments, there can be additional nucleotide residues 5′ or 3′to the TetO sequence(s), or there can be intervening nucleotide linkersequences, as long as the ability to bind TetR protein is noteliminated.

“Repression,” or “repressed,” within the context of the invention,refers to the interference of transcription of a gene of interest(encoding a protein of interest), occurring when TetR protein binds to aTetO binding site in the promoter that drives expression of the gene ofinterest, resulting in decreased expression of the protein of interestby the cell(s) (which are cell(s) that express TetR). Expression of agene of interest or of a protein of interest is said to be“derepressed,” when, in the presence of tetracycline in the medium,expression of the protein of interest is at least 1.5-fold over thebasal levels of expression by the cell(s) in the absence of tetracyclinein the medium.

“Tetracycline” means tetracycline or an analog of tetracycline, such asdoxycycline, anhydrotetracycline, minocycline, oxytetracycline,methacycline, chlortetracycline, or COL-3 (Chemically modifiedtetracycline-3).

The recombinant expression vectors of the present invention canoptionally contain one or more insulator elements, if desired.“Insulator elements,” or interchangeably, “insulator sequences,” are DNAsequences that protect transcription units from outside regulatoryinfluence. When placed between a transcription unit and an enhancersequence, these elements can block the action of the enhancer sequenceon the transcription unit. In constructs where insulator sequences flanka transcription unit, they can confer position independent expressionwhen transfected in cells. Many insulator elements have been identifiedand characterized including the chicken HS4, mouse H19, and Xenopus ARS.(See, e.g., Kanduri, C. et al., The 5′ flank of mouse H19 in an unusualchromatin conformation unidirectionally blocks enhancer-promotercommunication, Current Biology 10(8):449-457 (2000); Recillas-Targa, F.et al., Position-effect protection and enhancer blocking by the chickenbeta-globin insulator are separable activities. Proc. Nat. Acad. Sci.USA 99(10):6883-6888 (2002); Valenzuela, L., & Kamakaka, R. T.,Chromatin Insulators, Annu. Rev. Genet. 40:107-38 (2006); Watanabe, S.et al., Functional analysis of the sea urchin-derived arylsulfatase(Ars)-element in mammalian cells. Genes to Cells, 11(9), 1009-1021(2006)).

A rat EF-1alpha intron sequence useful in the inventive hybrid promotercomprises a nucleotide sequence at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% identical to the nucleotidesequence of SEQ ID NO:4:

SEQ ID NO: 4 GTGAGTGGCGGGTGTGGCTTCCGCGGGCCCCGGAGCTGGAGCCCTGCTCTGAGCGGGCCGGGCTGATATGCGAGTGTCGTCCGCAGGGTTTAGCTGTGAGCATTCCCACTTCGAGTGGCGGGCGGTGCGGGGGTGAGAGTGCGAGGCCTAGCGGCAACCCCGTAGCCTCGCCTCGTGTCCGGCTTGAGGCCTAGCGTGGTGTCCGCCGCCGCGTGCCACTCCGGCCGCACTATGCGTTTTTTGTCCTTGCTGCCCTCGATTGCCTTCCAGCAGCATGGGCTAACAAAGGGAGGGTGTGGGGCTCACTCTTAAGGAGCCCATGAAGCTTACGTTGGATAGGAATGGAAGGGCAGGAGGGGCGACTGGGGCCCGCCCGCCTTCGGAGCACATGTCCGACGCCACCTGGATGGGGCGAGGCCTGTGGCTTTCCGAAGCAATCGGGCGTGAGTTTAGCCTACCTGGGCCATGTGGCCCTAGCACTGGGCACGGTCTGGCCTGGCGGTGCCGCGTTCCCTTGCCTCCCAACAAGGGTGAGGCCGTCCCGCCCGGCACCAGTTGCTTGCGCGGAAAGATGGCCGCTCCCGGGGCCCTGTTGCAAGGAGCTCAAAATGGAGGACGCGGCAGCCCGGTGGAGCGGGCGGGTGAGTCACCCACACAAAGGAAGAGGGCCTTGCCCCTCGCCGGCCGCTGCTTCCTGTGACCCCGTGGTCTATCGGCCGCATAGTCACCTCGGGCTTCTCTTGAGCACCGCTCGTCGCGGCGGGGGGAGGGGATCTAATGGCGTTGGAGTTTGTTCACATTTGGTGGGTGGAGACTAGTCAGGCCAGCCTGGCGCTGGAAGTCATTCTTGGAATTTGCCCCTTTGAGTTTGGAGCGAGGCTAATTCTCAAGCCTCTTAGCGGTTCAAAGGTATTTTCTAAACCC GTTTCCAG//.

The inventive hybrid promoter also includes an intervening first leadersequence, operably linked 3′ to the mCMV enhancer and 5′ to theEF-1alpha intron sequence in an operable orientation. The interveningfirst leader sequence is about 10 to 200 nucleotide residues inlength—more preferably about 10 to 60 nucleotide residues in length oreven more preferably about 20-50 nucleotide residues in length—and lacksany secondary structure with stability greater than 20 kcal and lacksany ATG translational start sites. An example of a useful first leadersequence is an untranslated (5′UTR) leader sequence derived fromadenovirus tripartite leader (TPL), i.e., the nucleotide sequence of SEQID NO:3:

SEQ ID NO: 3 TACCTCTTCCGCATCGCTGTCTGCGAGGGCCAGCTGTTGGG//.

The inventive hybrid promoter also includes a second leader sequenceoperably linked 3′ to the EF-1 alpha intron sequence in an operableorientation. The second leader sequence is about 5 to 200 nucleotideresidues in length—more preferably about 10 to 200 nucleotide residuesin length or even more preferably about 10-150 nucleotide residues inlength—and lacks any secondary structure with stability greater than 20kcal and lacks any ATG translational start sites. An example of a usefulsecond leader sequence is another untranslated (5′UTR) leader sequenceregion derived from adenovirus tripartite leader (TPL), i.e., thenucleotide sequence of SEQ ID NO:5:

SEQ ID NO: 5 CTCGCGGTTGAGGACAAACTCTTCGCGGTCTTTCCAGTACTCTTGGATCGGAAACCCGTCGGCCTCCGAACGGTACTCCGCCACCGAGGGACCTGAGCGAGTCCGCATCGACCGGATCGGAAAACCTC//.

For other examples of useful leader sequences and design principles,see, e.g., Mignone, F. et al., Untranslated regions of mRNAs. GenomeBiology, 3(3): reviews0004.1-0004.10 (2002)), incorporated herein byreference in its entirety. Any suitable leader sequences, with the abovementioned characteristics, can be used in practicing the presentinvention.

One useful embodiment of the inventive hybrid promoter is a promoterthat comprises a nucleotide sequence at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% identical to thenucleotide sequence of SEQ ID NO:1, following, which contains mCMVGenBank: L06816.1, nucleotides 4067-4682, Rat EF-1alpha intron Genbank:AC158987.3, nucleotides 22137-21728; and an intervening first leadersequence underlined in lower case letters (SEQ ID NO:3); and a secondleader sequence underlined in italic lower case letters (SEQ ID NO:5):

SEQ ID NO: 1 GTCAACAGGAAAGTTCCATTGGAGCCAAGTACATTGAGTCAATAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATGGGAGGTAAGCCAATGGGTTTTTCCCATTACTGGCACGTATACTGAGTCATTAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATAGGGGTGAATCAACAGGAAAGTCCCATTGGAGCCAAGTACACTGAGTCAATAGGGACTTTCCATTGGGTTTTGCCCAGTACAAAAGGTCAATAGGGGGTGAGTCAATGGGTTTTTCCCATTATTGGCACGTACATAAGGTCAATAGGGGTGAGTCATTGGGTTTTTCCAGCCAATTTAATTAAAACGCCATGTACTTTCCCACCATTGACGTCAATGGGCTATTGAAACTAATGCAACGTGACCTTTAAACGGTACTTTCCCATAGCTGATTAATGGGAAAGTACCGTTCTCGAGCCAATACACGTCAATGGGAAGTGAAAGGGCAGCCAAAACGTAACACCGCCCCGGTTTTCCCCTGGAAATTCCATATTGGCACGCATTCTATTGGCTGAGCTGCGTTCTACGTGGGTATAAGAGGCGCGACCAGCGTCGGTACCGtacctcttccgcatcgctgtctgcgagggccagctgttgggGTGAGTGGCGGGTGTGGCTTCCGCGGGCCCCGGAGCTGGAGCCCTGCTCTGAGCGGGCCGGGCTGATATGCGAGTGTCGTCCGCAGGGTTTAGCTGTGAGCATTCCCACTTCGAGTGGCGGGCGGTGCGGGGGTGAGAGTGCGAGGCCTAGCGGCAACCCCGTAGCCTCGCCTCGTGTCCGGCTTGAGGCCTAGCGTGGTGTCCGCCGCCGCGTGCCACTCCGGCCGCACTATGCGTTTTTTGTCCTTGCTGCCCTCGATTGCCTTCCAGCAGCATGGGCTAACAAAGGGAGGGTGTGGGGCTCACTCTTAAGGAGCCCATGAAGCTTACGTTGGATAGGAATGGAAGGGCAGGAGGGGCGACTGGGGCCCGCCCGCCTTCGGAGCACATGTCCGACGCCACCTGGATGGGGCGAGGCCTGTGGCTTTCCGAAGCAATCGGGCGTGAGTTTAGCCTACCTGGGCCATGTGGCCCTAGCACTGGGCACGGTCTGGCCTGGCGGTGCCGCGTTCCCTTGCCTCCCAACAAGGGTGAGGCCGTCCCGCCCGGCACCAGTTGCTTGCGCGGAAAGATGGCCGCTCCCGGGGCCCTGTTGCAAGGAGCTCAAAATGGAGGACGCGGCAGCCCGGTGGAGCGGGCGGGTGAGTCACCCACACAAAGGAAGAGGGCCTTGCCCCTCGCCGGCCGCTGCTTCCTGTGACCCCGTGGTCTATCGGCCGCATAGTCACCTCGGGCTTCTCTTGAGCACCGCTCGTCGCGGCGGGGGGAGGGGATCTAATGGCGTTGGAGTTTGTTCACATTTGGTGGGTGGAGACTAGTCAGGCCAGCCTGGCGCTGGAAGTCATTCTTGGAATTTGCCCCTTTGAGTTTGGAGCGAGGCTAATTCTCAAGCCTCTTAGCGGTTCAAAGGTATTTTCTAAACCCGTTTCCAG ctcgcgttgaggacaaactcttcgcggtctttccagtactcttggatcggaaacccgtcggcctccgaacggtactccgccaccgagggacctgagcgagtccgcatcgaccggatcggaaaacctc //.

Examples of additional useful embodiments of the inventive hybridpromoter include (i) SEQ ID NO:30 (hybrid promoter sequence includingTetO, as in pJV57), (ii) SEQ ID NO:31 (hybrid promoter including a mCMVenhancer element with optimized hCMV promoter sequence, as in pJV59),and (iii) SEQ ID NO:32 (hybrid promoter including mCMV enhancer elementwith optimized hCMV promoter sequence and optimized TetO sequence, as inpJV60):

SEQ ID NO: 30 GTCAACAGGAAAGTTCCATTGGAGCCAAGTACATTGAGTCAATAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATGGGAGGTAAGCCAATGGGTTTTTCCCATTACTGGCACGTATACTGAGTCATTAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATAGGGGTGAATCAACAGGAAAGTCCCATTGGAGCCAAGTACACTGAGTCAATAGGGACTTTCCATTGGGTTTTGCCCAGTACAAAAGGTCAATAGGGGGTGAGTCAATGGGTTTTTCCCATTATTGGCACGTACATAAGGTCAATAGGGGTGAGTCATTGGGTTTTTCCAGCCAATTTAATTAAAACGCCATGTACTTTCCCACCATTGACGTCAATGGGCTATTGAAACTAATGCAACGTGACCTTTAAACGGTACTTTCCCATAGCTGATTAATGGGAAAGTACCGTTCTCGAGCCAATACACGTCAATGGGAAGTGAAAGGGCAGCCAAAACGTAACACCGCCCCGGTTTTCCCCTGGAAATTCCATATTGGCACGCATTCTATTGGCTGAGCTGCGTTCTACGTGGGTATATAAGCAGAGCTCTCCCTATCAGTGATAGAGATCTCCCTATCAGTGATAGAGATCGTCGACGAGCTCAGCGTCGGTACCGTACCTCTTCCGCATCGCTGTCTGCGAGGGCCAGCTGTTGGGGTGAGTGGCGGGTGTGGCTTCCGCGGGCCCCGGAGCTGGAGCCCTGCTCTGAGCGGGCCGGGCTGATATGCGAGTGTCGTCCGCAGGGTTTAGCTGTGAGCATTCCCACTTCGAGTGGCGGGCGGTGCGGGGGTGAGAGTGCGAGGCCTAGCGGCAACCCCGTAGCCTCGCCTCGTGTCCGGCTTGAGGCCTAGCGTGGTGTCCGCCGCCGCGTGCCACTCCGGCCGCACTATGCGTTTTTTGTCCTTGCTGCCCTCGATTGCCTTCCAGCAGCATGGGCTAACAAAGGGAGGGTGTGGGGCTCACTCTTAAGGAGCCCATGAAGCTTACGTTGGATAGGAATGGAAGGGCAGGAGGGGCGACTGGGGCCCGCCCGCCTTCGGAGCACATGTCCGACGCCACCTGGATGGGGCGAGGCCTGTGGCTTTCCGAAGCAATCGGGCGTGAGTTTAGCCTACCTGGGCCATGTGGCCCTAGCACTGGGCACGGTCTGGCCTGGCGGTGCCGCGTTCCCTTGCCTCCCAACAAGGGTGAGGCCGTCCCGCCCGGCACCAGTTGCTTGCGCGGAAAGATGGCCGCTCCCGGGGCCCTGTTGCAAGGAGCTCAAAATGGAGGACGCGGCAGCCCGGTGGAGCGGGCGGGTGAGTCACCCACACAAAGGAAGAGGGCCTTGCCCCTCGCCGGCCGCTGCTTCCTGTGACCCCGTGGTCTATCGGCCGCATAGTCACCTCGGGCTTCTCTTGAGCACCGCTCGTCGCGGCGGGGGGAGGGGATCTAATGGCGTTGGAGTTTGTTCACATTTGGTGGGTGGAGACTAGTCAGGCCAGCCTGGCGCTGGAAGTCATTCTTGGAATTTGCCCCTTTGAGTTTGGAGCGAGGCTAATTCTCAAGCCTCTTAGCGGTTCAAAGGTATTTTCTAAACCCGTTTCCAGCTCGCGGTTGAGGACAAACTCTTCGCGGTCTTTCCAGTACTCTTGGATCGGAAACCCGTCGGCCTCCGAACGGTACTCCGCCACCGAGGGACCTGAGCGAGTCCGCATCGACCGGATCGG AAAACCTC//; SEQ ID NO: 31GTCAACAGGAAAGTTCCATTGGAGCCAAGTACATTGAGTCAATAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATGGGAGGTAAGCCAATGGGTTTTTCCCATTACTGGCACGTATACTGAGTCATTAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATAGGGGTGAATCAACAGGAAAGTCCCATTGGAGCCAAGTACACTGAGTCAATAGGGACTTTCCATTGGGTTTTGCCCAGTACAAAAGGTCAATAGGGGGTGAGTCAATGGGTTTTTCCCATTATTGGCACGTACATAAGGTCAATAGGGGTGAGTCATTGGGTTTTTCCAGCCAATTTAATTAAAACGCCATGTACTTTCCCACCATTGACGTCAATGGGCTATTGAAACTAATGCAACGTGACCTTTAAACGGTACTTTCCCATAGCTGATTAATGGGAAAGTACCGTTCTCGAGCCAATACACGTCAATGGGAAGTGAAAGGGCAGCCAAAACGTAACACCGCCCCGGTTTTCCCCTGGAAATTCCATATTGGCACGCATTCTATTGGCTGAGCTGCGTTCTACGTGGGTATATAAGCAGAGCTCGTTTAGTGAACCGTCAGTTCGTCTCTAGACGCCAACCGCCTCTTCCGCATCGCTGTCTGCGAGGGCCAGCTGTTGGGGTGAGTGGCGGGTGTGGCTTCCGCGGGCCCCGGAGCTGGAGCCCTGCTCTGAGCGGGCCGGGCTGATATGCGAGTGTCGTCCGCAGGGTTTAGCTGTGAGCATTCCCACTTCGAGTGGCGGGCGGTGCGGGGGTGAGAGTGCGAGGCCTAGCGGCAACCCCGTAGCCTCGCCTCGTGTCCGGCTTGAGGCCTAGCGTGGTGTCCGCCGCCGCGTGCCACTCCGGCCGCACTATGCGTTTTTTGTCCTTGCTGCCCTCGATTGCCTTCCAGCAGCATGGGCTAACAAAGGGAGGGTGTGGGGCTCACTCTTAAGGAGCCCATGAAGCTTACGTTGGATAGGAATGGAAGGGCAGGAGGGGCGACTGGGGCCCGCCCGCCTTCGGAGCACATGTCCGACGCCACCTGGATGGGGCGAGGCCTGTGGCTTTCCGAAGCAATCGGGCGTGAGTTTAGCCTACCTGGGCCATGTGGCCCTAGCACTGGGCACGGTCTGGCCTGGCGGTGCCGCGTTCCCTTGCCTCCCAACAAGGGTGAGGCCGTCCCGCCCGGCACCAGTTGCTTGCGCGGAAAGATGGCCGCTCCCGGGGCCCTGTTGCAAGGAGCTCAAAATGGAGGACGCGGCAGCCCGGTGGAGCGGGCGGGTGAGTCACCCACACAAAGGAAGAGGGCCTTGCCCCTCGCCGGCCGCTGCTTCCTGTGACCCCGTGGTCTATCGGCCGCATAGTCACCTCGGGCTTCTCTTGAGCACCGCTCGTCGCGGCGGGGGGAGGGGATCTAATGGCGTTGGAGTTTGTTCACATTTGGTGGGTGGAGACTAGTCAGGCCAGCCTGGCGCTGGAAGTCATTCTTGGAATTTGCCCCTTTGAGTTTGGAGCGAGGCTAATTCTCAAGCCTCTTAGCGGTTCAAAGGTATTTTCTAAACCCGTTTCCAGCTCGCGGTTGAGGACAAACTCTTCGCGGTCTTTCCAGTACTCTTGGATCGGAAACCCGTCGGCCTCCGAACGGTACTCCGCCACCGAGGGACCTGAGCGAGTCCGCAT CGACCGGATCGGAAAACCTC//; andSEQ ID NO: 32 GTCAACAGGAAAGTTCCATTGGAGCCAAGTACATTGAGTCAATAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATGGGAGGTAAGCCAATGGGTTTTTCCCATTACTGGCACGTATACTGAGTCATTAGGGACTTTCCAATGGGTTTTGCCCAGTACATAAGGTCAATAGGGGTGAATCAACAGGAAAGTCCCATTGGAGCCAAGTACACTGAGTCAATAGGGACTTTCCATTGGGTTTTGCCCAGTACAAAAGGTCAATAGGGGGTGAGTCAATGGGTTTTTCCCATTATTGGCACGTACATAAGGTCAATAGGGGTGAGTCATTGGGTTTTTCCAGCCAATTTAATTAAAACGCCATGTACTTTCCCACCATTGACGTCAATGGGCTATTGAAACTAATGCAACGTGACCTTTAAACGGTACTTTCCCATAGCTGATTAATGGGAAAGTACCGTTCTCGAGCCAATACACGTCAATGGGAAGTGAAAGGGCAGCCAAAACGTAACACCGCCCCGGTTTTCCCCTGGAAATTCCATATTGGCACGCATTCTATTGGCTGAGCTGCGTTCTACGTGGGTATATAAGCAGAGCTCTCCCTATCAGTGATCAGTTCCTCCCTATCAGTGATAGAGATCGTCGACGAGCTCAGCGTCGGTACCGTACCTCTTCCGCATCGCTGTCTGCGAGGGCCAGCTGTTGGGGTGAGTGGCGGGTGTGGCTTCCGCGGGCCCCGGAGCTGGAGCCCTGCTCTGAGCGGGCCGGGCTGATATGCGAGTGTCGTCCGCAGGGTTTAGCTGTGAGCATTCCCACTTCGAGTGGCGGGCGGTGCGGGGGTGAGAGTGCGAGGCCTAGCGGCAACCCCGTAGCCTCGCCTCGTGTCCGGCTTGAGGCCTAGCGTGGTGTCCGCCGCCGCGTGCCACTCCGGCCGCACTATGCGTTTTTTGTCCTTGCTGCCCTCGATTGCCTTCCAGCAGCATGGGCTAACAAAGGGAGGGTGTGGGGCTCACTCTTAAGGAGCCCATGAAGCTTACGTTGGATAGGAATGGAAGGGCAGGAGGGGCGACTGGGGCCCGCCCGCCTTCGGAGCACATGTCCGACGCCACCTGGATGGGGCGAGGCCTGTGGCTTTCCGAAGCAATCGGGCGTGAGTTTAGCCTACCTGGGCCATGTGGCCCTAGCACTGGGCACGGTCTGGCCTGGCGGTGCCGCGTTCCCTTGCCTCCCAACAAGGGTGAGGCCGTCCCGCCCGGCACCAGTTGCTTGCGCGGAAAGATGGCCGCTCCCGGGGCCCTGTTGCAAGGAGCTCAAAATGGAGGACGCGGCAGCCCGGTGGAGCGGGCGGGTGAGTCACCCACACAAAGGAAGAGGGCCTTGCCCCTCGCCGGCCGCTGCTTCCTGTGACCCCGTGGTCTATCGGCCGCATAGTCACCTCGGGCTTCTCTTGAGCACCGCTCGTCGCGGCGGGGGGAGGGGATCTAATGGCGTTGGAGTTTGTTCACATTTGGTGGGTGGAGACTAGTCAGGCCAGCCTGGCGCTGGAAGTCATTCTTGGAATTTGCCCCTTTGAGTTTGGAGCGAGGCTAATTCTCAAGCCTCTTAGCGGTTCAAAGGTATTTTCTAAACCCGTTTCCAGCTCGCGGTTGAGGACAAACTCTTCGCGGTCTTTCCAGTACTCTTGGATCGGAAACCCGTCGGCCTCCGAACGGTACTCCGCCACCGAGGGACCTGAGCGAGTCCGCATCGACCGGATCGG AAAACCTC//.

The terms “in operable combination”, “in operable order” and “operablylinked” as used herein refer to the linkage of nucleic acid sequences insuch a manner that a nucleic acid molecule capable of directing thetranscription of a given gene and/or the synthesis of a desired proteinmolecule is produced. The term also refers to the linkage of amino acidsequences in such a manner so that a functional protein is produced. Forexample, a control sequence in a vector that is “operably linked” to aprotein coding sequence is ligated thereto so that expression of theprotein coding sequence is achieved under conditions compatible with thetranscriptional activity of the control sequences.

“Polypeptide” and “protein” are used interchangeably herein and includea molecular chain of two or more amino acids linked covalently throughpeptide bonds. The terms do not refer to a specific length of theproduct. Thus, “peptides,” and “oligopeptides,” are included within thedefinition of polypeptide. The terms include post-translationalmodifications of the polypeptide, for example, glycosylations,acetylations, phosphorylations and the like. In addition, proteinfragments, analogs, mutated or variant proteins, fusion proteins and thelike are included within the meaning of polypeptide. The terms alsoinclude molecules in which one or more amino acid analogs ornon-canonical or unnatural amino acids are included as can be expressedrecombinantly using known protein engineering techniques. In addition,fusion proteins can be derivatized as described herein by well-knownorganic chemistry techniques.

A “variant” of a polypeptide (e.g., an immunoglobulin, or an antibody)comprises an amino acid sequence wherein one or more amino acid residuesare inserted into, deleted from and/or substituted into the amino acidsequence relative to another polypeptide sequence. Variants includefusion proteins.

The term “fusion protein” indicates that the protein includespolypeptide components derived from more than one parental protein orpolypeptide. Typically, a fusion protein is expressed from a “fusiongene” in which a nucleotide sequence encoding a polypeptide sequencefrom one protein is appended in frame with, and optionally separated bya linker from, a nucleotide sequence encoding a polypeptide sequencefrom a different protein. The fusion gene can then be expressed by arecombinant host cell as a single protein.

A “secreted” protein refers to those proteins capable of being directedto the ER, secretory vesicles, or the extracellular space as a result ofa secretory signal peptide sequence, as well as those proteins releasedinto the extracellular space without necessarily containing a signalsequence. If the secreted protein is released into the extracellularspace, the secreted protein can undergo extracellular processing toproduce a “mature” protein. Release into the extracellular space canoccur by many mechanisms, including exocytosis and proteolytic cleavage.In some other embodiments of the inventive method, the protein ofinterest can be synthesized by the host cell as a secreted protein,which can then be further purified from the extracellular space and/ormedium.

As used herein “soluble” when in reference to a protein produced byrecombinant DNA technology in a host cell is a protein that exists inaqueous solution; if the protein contains a twin-arginine signal aminoacid sequence the soluble protein is exported to the periplasmic spacein gram negative bacterial hosts, or is secreted into the culture mediumby eukaryotic host cells capable of secretion, or by bacterial hostpossessing the appropriate genes (e.g., the kil gene). Thus, a solubleprotein is a protein which is not found in an inclusion body inside thehost cell. Alternatively, depending on the context, a soluble protein isa protein which is not found integrated in cellular membranes, or, invitro, is dissolved, or is capable of being dissolved in an aqueousbuffer under physiological conditions without forming significantamounts of insoluble aggregates (i.e., forms aggregates less than 10%,and typically less than about 5%, of total protein) when it is suspendedwithout other proteins in an aqueous buffer of interest underphysiological conditions, such buffer not containing a detergent orchaotropic agent, such as urea, guanidinium hydrochloride, or lithiumperchlorate. In contrast, an insoluble protein is one which exists indenatured form inside cytoplasmic granules (called an inclusion body) inthe host cell, or again depending on the context, an insoluble proteinis one which is present in cell membranes, including but not limited to,cytoplasmic membranes, mitochondrial membranes, chloroplast membranes,endoplasmic reticulum membranes, etc., or in an in vitro aqueous bufferunder physiological conditions forms significant amounts of insolubleaggregates (i.e., forms aggregates equal to or more than about 10% oftotal protein) when it is suspended without other proteins (atphysiologically compatible temperature) in an aqueous buffer of interestunder physiological conditions, such buffer not containing a detergentor chaotropic agent, such as urea, guanidinium hydrochloride, or lithiumperchlorate.

The term “polynucleotide” or “nucleic acid” includes bothsingle-stranded and double-stranded nucleotide polymers containing twoor more nucleotide residues. The nucleotide residues comprising thepolynucleotide can be ribonucleotides or deoxyribonucleotides or amodified form of either type of nucleotide. Said modifications includebase modifications such as bromouridine and inosine derivatives, ribosemodifications such as 2′,3′-dideoxyribose, and internucleotide linkagemodifications such as phosphorothioate, phosphorodithioate,phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,phosphoraniladate and phosphoroamidate.

The term “oligonucleotide” means a polynucleotide comprising 200 orfewer nucleotide residues. In some embodiments, oligonucleotides are 10to 60 bases in length. In other embodiments, oligonucleotides are 12,13, 14, 15, 16, 17, 18, 19, or 20 to 40 nucleotides in length.Oligonucleotides may be single stranded or double stranded, e.g., foruse in the construction of a mutant gene. Oligonucleotides may be senseor antisense oligonucleotides. An oligonucleotide can include a label,including a radiolabel, a fluorescent label, a hapten or an antigeniclabel, for detection assays. Oligonucleotides may be used, for example,as PCR primers, cloning primers or hybridization probes.

A “polynucleotide sequence” or “nucleotide sequence” or “nucleic acidsequence,” as used interchangeably herein, is the primary sequence ofnucleotide residues in a polynucleotide, including of anoligonucleotide, a DNA, and RNA, a nucleic acid, or a character stringrepresenting the primary sequence of nucleotide residues, depending oncontext. From any specified polynucleotide sequence, either the givennucleic acid or the complementary polynucleotide sequence can bedetermined. Included are DNA or RNA of genomic or synthetic origin whichmay be single- or double-stranded, and represent the sense or antisensestrand. Unless specified otherwise, the left-hand end of anysingle-stranded polynucleotide sequence discussed herein is the 5′ end;the left-hand direction of double-stranded polynucleotide sequences isreferred to as the 5′ direction. The direction of 5′ to 3′ addition ofnascent RNA transcripts is referred to as the transcription direction;sequence regions on the DNA strand having the same sequence as the RNAtranscript that are 5′ to the 5′ end of the RNA transcript are referredto as “upstream sequences;” sequence regions on the DNA strand havingthe same sequence as the RNA transcript that are 3′ to the 3′ end of theRNA transcript are referred to as “downstream sequences.”

As used herein, an “isolated nucleic acid molecule” or “isolated nucleicacid sequence” is a nucleic acid molecule that is either (1) identifiedand separated from at least one contaminant nucleic acid molecule withwhich it is ordinarily associated in the natural source of the nucleicacid or (2) cloned, amplified, tagged, or otherwise distinguished frombackground nucleic acids such that the sequence of the nucleic acid ofinterest can be determined. An isolated nucleic acid molecule is otherthan in the form or setting in which it is found in nature. However, anisolated nucleic acid molecule includes a nucleic acid moleculecontained in cells that ordinarily express the immunoglobulin (e.g.,antibody) where, for example, the nucleic acid molecule is in achromosomal location different from that of natural cells.

As used herein, the terms “nucleic acid molecule encoding,” “DNAsequence encoding,” and “DNA encoding” refer to the order or sequence ofdeoxyribonucleotides along a strand of deoxyribonucleic acid. The orderof these deoxyribonucleotides determines the order of ribonucleotidesalong the mRNA chain, and also determines the order of amino acids alongthe polypeptide (protein) chain. The DNA sequence thus codes for the RNAsequence and for the amino acid sequence.

The term “gene” is used broadly to refer to any nucleic acid associatedwith a biological function. Genes typically include coding sequencesand/or the regulatory sequences required for expression of such codingsequences. The term “gene” applies to a specific genomic or recombinantsequence, as well as to a cDNA or mRNA encoded by that sequence. Genesalso include non-expressed nucleic acid segments that, for example, formrecognition sequences for other proteins. Non-expressed regulatorysequences including transcriptional control elements to which regulatoryproteins, such as transcription factors, bind, resulting intranscription of adjacent or nearby sequences.

“Expression of a gene” or “expression of a nucleic acid” meanstranscription of DNA into RNA (optionally including modification of theRNA, e.g., splicing), translation of RNA into a polypeptide (possiblyincluding subsequent post-translational modification of thepolypeptide), or both transcription and translation, as indicated by thecontext.

The present invention relates to an expression cassette that includesthe inventive hybrid promoter. A eukaryotic “expression cassette” refersto the part of an expression vector that enables production of proteinin a eukaryotic cell, such as a mammalian cell. It includes a promoter,operable in a eukaryotic cell, for mRNA transcription, one or moregene(s) encoding protein(s) of interest and a mRNA termination andprocessing signal. An expression cassette can usefully include among thecoding sequences, a gene useful as a selective marker. In the expressioncassette of the present invention, the hybrid promoter (or controlsequence) is operably linked 5′ to an open reading frame encoding anexogenous protein of interest; and a polyadenylation site is operablylinked 3′ to the open reading frame. The protein of interest encoded bythe open reading frame can be a monomeric protein or fusion protein, orit can be a subunit of a larger multimeric protein. The protein ofinterest expressed from a second or third expression cassette can bedifferent or the same as the protein of interest encoded by the openreading frame of the first expression cassette; for example, a firstexpression cassette can include the coding sequence for a light chainsubunit of an immunoglobulin, and a second or third expression cassettein the expression vector can include the coding sequence for theimmunoglobulin heavy chain subunit, or vice versa, with each of thesubunits being the “protein of interest” with respect to the expressioncassette in which its coding sequence is included. One embodiment of auseful polyadenylation site sequence is a SV40 late polyadenylation siteSEQ ID NO:14:

SEQ ID NO: 14 CACACATCATAAGATACATTGATGAGTTTGGACAAACCACAACTAGAATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGTTCAGGGGGAGATGTGGGAGGTTTTTTAAAGCAAGTAAAACCTCTACAA ATGTGGTA//.

Other suitable control sequences can also be included as long as theexpression cassette remains operable. The open reading frame canoptionally include a coding sequence for more than one protein ofinterest.

As used herein the term “coding region” or “coding sequence” when usedin reference to a structural gene refers to the nucleotide sequenceswhich encode the amino acids found in the nascent polypeptide as aresult of translation of an mRNA molecule. The coding region is bounded,in eukaryotes, on the 5′ side by the nucleotide triplet “ATG” whichencodes the initiator methionine and on the 3′ side by one of the threetriplets which specify stop codons (i.e., TAA, TAG, TGA).

The present invention also encompasses a recombinant expression vectorcomprising the inventive expression cassette.

The term “vector” means any molecule or entity (e.g., nucleic acid,plasmid, bacteriophage or virus) used to transfer protein codinginformation into a host cell.

The term “expression vector” or “expression construct” as used hereinrefers to a recombinant DNA molecule containing a desired codingsequence and appropriate nucleic acid control sequences necessary forthe expression of the operably linked coding sequence in a particularhost cell. An expression vector can include, but is not limited to,sequences that affect or control transcription, translation, and, ifintrons are present, affect RNA splicing of a coding region operablylinked thereto. Nucleic acid sequences necessary for expression inprokaryotes include a promoter, optionally an operator sequence, aribosome binding site and possibly other sequences. Eukaryotic cells areknown to utilize promoters, enhancers, and termination andpolyadenylation signals. A secretory signal peptide sequence can also,optionally, be encoded by the expression vector, operably linked to thecoding sequence of interest, so that the expressed polypeptide can besecreted by the recombinant host cell, for more facile isolation of thepolypeptide of interest from the cell, if desired. Such techniques arewell known in the art. (E.g., Goodey, Andrew R.; et al., Peptide and DNAsequences, U.S. Pat. No. 5,302,697; Weiner et al., Compositions andmethods for protein secretion, U.S. Pat. Nos. 6,022,952 and 6,335,178;Uemura et al., Protein expression vector and utilization thereof, U.S.Pat. No. 7,029,909; Ruben et al., 27 human secreted proteins, US2003/0104400 A1). For expression of multi-subunit proteins of interest,separate expression vectors in suitable numbers and proportions, eachcontaining a coding sequence for each of the different monomers, can beused to transform a host cell. In other embodiments a single expressionvector can be used to express the different subunits of the protein ofinterest.

The present invention also relates to a mammalian host cell comprisingthe inventive recombinant expression vector.

The term “host cell” means a cell that has been transformed, or iscapable of being transformed, with a nucleic acid and thereby expressesa gene of interest. The term includes the progeny of the parent cell,whether or not the progeny is identical in morphology or in geneticmake-up to the original parent cell, so long as the gene of interest ispresent. Any of a large number of available and well-known host cellsmay be used in the practice of this invention. The selection of aparticular host is dependent upon a number of factors recognized by theart. These include, for example, compatibility with the chosenexpression vector, toxicity of the peptides encoded by the DNA molecule,rate of transformation, ease of recovery of the peptides, expressioncharacteristics, bio-safety and costs. A balance of these factors mustbe struck with the understanding that not all hosts may be equallyeffective for the expression of a particular DNA sequence. Within thesegeneral guidelines, useful microbial host cells in culture includebacteria (such as Escherichia coli sp.), yeast (such as Saccharomycessp.) and other fungal cells, insect cells, plant cells, mammalian(including human) cells, e.g., CHO cells and HEK-293 cells.Modifications can be made at the DNA level, as well. Thepeptide-encoding DNA sequence may be changed to codons more compatiblewith the chosen host cell. For E. coli, optimized codons are known inthe art. Codons can be substituted to eliminate restriction sites or toinclude silent restriction sites, which may aid in processing of the DNAin the selected host cell. Next, the transformed host is cultured andpurified. Host cells may be cultured under conventional fermentationconditions so that the desired compounds are expressed. Suchfermentation conditions are well known in the art.

Examples of useful mammalian host cell lines are Chinese hamster ovarycells, including CHO-K1 cells (e.g., ATCC CCL61), DXB-11, DG-44, andChinese hamster ovary cells/-DHFR (CHO, Urlaub et al, Proc. Natl. Acad.Sci. USA 77: 4216 (1980)); monkey kidney CV1 line transformed by SV40(COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cellssubcloned for growth in suspension culture, [Graham et al, J. Gen Virol.36: 59 (1977)]; baby hamster kidney cells (BHK, ATCC CCL 10); mouseSertoli cells (TM4, Mather, Biol. Reprod. 23: 243-251 (1980)); monkeykidney cells (CV1 ATCC CCL 70); African green monkey kidney cells(VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells(BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); humanhepatoma cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCCCCL51); TRI cells (Mather et al, Annals N.Y Acad. Sci. 383: 44-68(1982)); MRC 5 cells or FS4 cells; or mammalian myeloma cells.

“Cell,” “cell line,” and “cell culture” are often used interchangeablyand all such designations herein include cellular progeny. For example,a cell “derived” from a CHO cell is a cellular progeny of a ChineseHamster Ovary cell, which may be removed from the original primary cellparent by any number of generations, and which can also include atransformant progeny cell. Transformants and transformed cells includethe primary subject cell and cultures derived therefrom without regardfor the number of transfers. It is also understood that all progeny maynot be precisely identical in DNA content, due to deliberate orinadvertent mutations. Mutant progeny that have the same function orbiological activity as screened for in the originally transformed cellare included.

Host cells are transformed or transfected with the above-describednucleic acids or vectors for production of polypeptides (includingantigen binding proteins, such as antibodies) and are cultured inconventional nutrient medium modified as appropriate for inducingpromoters, selecting transformants, or amplifying the genes encoding thedesired sequences. In addition, novel vectors and transfected cell lineswith multiple copies of transcription units separated by a selectivemarker are particularly useful for the expression of polypeptides, suchas antibodies.

The term “transfection” means the uptake of foreign or exogenous DNA bya cell, and a cell has been “transfected” when the exogenous DNA hasbeen introduced inside the cell membrane. A number of transfectiontechniques are well known in the art and are disclosed herein. See,e.g., Graham et al., 1973, Virology 52:456; Sambrook et al., 2001,Molecular Cloning: A Laboratory Manual, supra; Davis et al., 1986, BasicMethods in Molecular Biology, Elsevier; Chu et al., 1981, Gene 13:197.Such techniques can be used to introduce one or more exogenous DNAmoieties into suitable host cells.

The term “transformation” refers to a change in a cell's geneticcharacteristics, and a cell has been transformed when it has beenmodified to contain new DNA or RNA. For example, a cell is transformedwhere it is genetically modified from its native state by introducingnew genetic material via transfection, transduction, or othertechniques. Following transfection or transduction, the transforming DNAmay recombine with that of the cell by physically integrating into achromosome of the cell, or may be maintained transiently as an episomalelement without being replicated, or may replicate independently as aplasmid. A cell is considered to have been “stably transformed” when thetransforming DNA is replicated with the division of the cell.

The present invention also relates to a method of producing a protein ofinterest involving culturing the mammalian host cell, in aqueous mediumunder physiological conditions permitting expression of the protein ofinterest; and recovering the protein of interest from the medium.

The host cells used to produce the polypeptides useful in the inventionmay be cultured in a variety of media. Commercially available media suchas Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma),RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM),Sigma) are suitable for culturing the host cells. In addition, any ofthe media described in Ham et al., Meth. Enz. 58: 44 (1979), Barnes etal., Anal. Biochem. 102: 255 (1980), U.S. Pat. Nos. 4,767,704;4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO90103430; WO 87/00195;or U.S. Pat. Re. No. 30,985 may be used as culture media for the hostcells. Any of these media may be supplemented as necessary with hormonesand/or other growth factors (such as insulin, transferrin, or epidermalgrowth factor), salts (such as sodium chloride, calcium, magnesium, andphosphate), buffers (such as HEPES), nucleotides (such as adenosine andthymidine), antibiotics (such as Gentamycin™ drug), trace elements(defined as inorganic compounds usually present at final concentrationsin the micromolar range), and glucose or an equivalent energy source,such that the physiological conditions of the cell in, or on, the mediumpromote expression of the protein of interest by the host cell; anyother necessary supplements may also be included at appropriateconcentrations that would be known to those skilled in the art. Theculture conditions, such as temperature (typically, but not necessarily,about 37° C.), pH (typically, but not necessarily, about pH 6.5-7.5),oxygenation, and the like, are those previously used with the host cellselected for expression of the protein of interest, and will be apparentto the ordinarily skilled artisan. The culture medium can include asuitable amount of serum such a fetal bovine serum (FBS), or preferably,the host cells can be adapted for culture in serum-free medium. In someembodiments, the aqueous medium is liquid, such that the host cells arecultured in a cell suspension within the liquid medium. The host cellscan be usefully grown in batch culture or in continuous culture systems.

In other embodiments, the mammalian host cells can be cultured on solidor semisolid aqueous medium, for example, containing agar or agarose, toform a medium or substrate surface to which the cells adhere and form anadhesion layer.

Upon culturing the host cells, the recombinant polypeptide can beproduced intracellularly, in the periplasmic space, or directly secretedinto the medium. If the polypeptide, such as an antigen binding protein(e.g., an antibody), is produced intracellularly, as a first step, theparticulate debris, either host cells or lysed fragments, is removed,for example, by centrifugation or ultrafiltration.

A protein of interest, such as an antibody or antibody fragment can bepurified using, for example, hydroxylapatite chromatography, cation oranion exchange chromatography, or preferably affinity chromatography,using the antigen of interest or protein A or protein G as an affinityligand. Protein A can be used to purify proteins that includepolypeptides are based on human γ1, γ2, or γ4 heavy chains (Lindmark etal., J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended forall mouse isotypes and for human γ3 (Guss et al, EMBO J. 5: 15671575(1986)). The matrix to which the affinity ligand is attached is mostoften agarose, but other matrices are available. Mechanically stablematrices such as controlled pore glass or poly(styrenedivinyl)benzeneallow for faster flow rates and shorter processing times than can beachieved with agarose. Where the protein comprises a CH 3 domain, theBakerbond ABX™ resin (J. T. Baker, Phillipsburg, N.J.) is useful forpurification. Other techniques for protein purification such as ethanolprecipitation, Reverse Phase HPLC, chromatofocusing, SDS-PAGE, andammonium sulfate precipitation are also possible depending on theantibody to be recovered.

“Under physiological conditions” with respect to incubating buffers andimmunoglobulins, or other binding assay reagents means incubation underconditions of temperature, pH, and ionic strength, that permit abiochemical reaction, such as a non-covalent binding reaction, to occur.Typically, the temperature is at room or ambient temperature up to about37° C. and at pH 6.5-7.5.

“Physiologically acceptable salt” of a composition of matter, forexample a salt of an immunoglobulin, such as an antibody, or otherprotein of interest, means any salt, or salts, that are known or laterdiscovered to be pharmaceutically acceptable. Some non-limiting examplesof pharmaceutically acceptable salts are: acetate; trifluoroacetate;hydrohalides, such as hydrochloride and hydrobromide; sulfate; citrate;maleate; tartrate; glycolate; gluconate; succinate; mesylate; besylate;salts of gallic acid esters (gallic acid is also known as 3,4, 5trihydroxybenzoic acid) such as PentaGalloylGlucose (PGG) andepigallocatechin gallate (EGCG), salts of cholesteryl sulfate, pamoate,tannate and oxalate salts.

A “reaction mixture” is an aqueous mixture containing all the reagentsand factors necessary, which under physiological conditions ofincubation, permit an in vitro biochemical reaction of interest tooccur, such as a covalent or non-covalent binding reaction.

A “domain” or “region” (used interchangeably herein) of a polynucleotideis any portion of the entire polynucleotide, up to and including thecomplete polynucleotide, but typically comprising less than the completepolynucleotide. A domain can, but need not, fold independently (e.g.,DNA hairpin folding) of the rest of the polynucleotide chain and/or becorrelated with a particular biological, biochemical, or structuralfunction or location, such as a coding region or a regulatory region.

A “domain” or “region” (used interchangeably herein) of a protein is anyportion of the entire protein, up to and including the complete protein,but typically comprising less than the complete protein. A domain can,but need not, fold independently of the rest of the protein chain and/orbe correlated with a particular biological, biochemical, or structuralfunction or location (e.g., a ligand binding domain, or a cytosolic,transmembrane or extracellular domain).

The term “antibody”, or interchangeably “Ab”, is used in the broadestsense and includes fully assembled antibodies, monoclonal antibodies(including human, humanized or chimeric antibodies), polyclonalantibodies, multispecific antibodies (e.g., bispecific antibodies), andantibody fragments that can bind antigen (e.g., Fab, Fab′, F(ab′)₂, Fv,single chain antibodies, diabodies), comprising complementaritydetermining regions (CDRs) of the foregoing as long as they exhibit thedesired biological activity. Multimers or aggregates of intact moleculesand/or fragments, including chemically derivatized antibodies, arecontemplated. Antibodies of any isotype class or subclass, includingIgG, IgM, IgD, IgA, and IgE, IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2, orany allotype, are contemplated. Different isotypes have differenteffector functions; for example, IgG1 and IgG3 isotypes haveantibody-dependent cellular cytotoxicity (ADCC) activity.

An “isolated” protein, e.g., an immunoglobulin, such as an antibody orantibody fragment, is one that has been identified and separated fromone or more components of its natural environment or of a culture mediumin which it has been secreted by a producing cell. In some embodiments,the isolated protein is substantially free from proteins or polypeptidesor other contaminants that are found in its natural or culture mediumenvironment that would interfere with its therapeutic, diagnostic,prophylactic, research or other use. “Contaminant” components of itsnatural environment or medium are materials that would interfere withdiagnostic or therapeutic uses for the protein, e.g., an antibody, andmay include enzymes, hormones, and other proteinaceous ornonproteinaceous (e.g., polynucleotides, lipids, carbohydrates) solutes.Typically, an “isolated protein” constitutes at least about 5%, at leastabout 10%, at least about 25%, or at least about 50% of a given sample.In some embodiments, the protein of interest, e.g., an antibody will bepurified (1) to greater than 95% by weight of protein, and mostpreferably more than 99% by weight, or (2) to homogeneity by SDS-PAGEunder reducing or nonreducing conditions, optionally using a stain,e.g., Coomassie blue or silver stain. Isolated naturally occurringantibody includes the antibody in situ within recombinant cells since atleast one component of the protein's natural environment will not bepresent. Typically, however, the isolated protein of interest (e.g., anantibody) will be prepared by at least one purification step.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. Monoclonal antibodies that are antigen binding proteinsare highly specific binders, being directed against an individualantigenic site or epitope, in contrast to polyclonal antibodypreparations that typically include different antibodies directedagainst different epitopes. Nonlimiting examples of monoclonalantibodies include murine, rabbit, rat, chicken, chimeric, humanized, orhuman antibodies, fully assembled antibodies, multispecific antibodies(including bispecific antibodies), antibody fragments that can bind anantigen (including, Fab, Fab′, F(ab)₂, Fv, single chain antibodies,diabodies), maxibodies, nanobodies, and recombinant peptides comprisingCDRs of the foregoing as long as they exhibit the desired biologicalactivity, or variants or derivatives thereof.

The modifier “monoclonal” indicates the character of the antibody asbeing obtained from a substantially homogeneous population ofantibodies, and is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies to be used in accordance with the present invention may bemade by the hybridoma method first described by Kohler et al., Nature,256:495 [1975], or may be made by recombinant DNA methods (see, e.g.,U.S. Pat. No. 4,816,567). The “monoclonal antibodies” may also beisolated from phage antibody libraries using the techniques described inClackson et al., Nature, 352:624-628 [1991] and Marks et al., J. Mol.Biol., 222:581-597 (1991), for example.

A “multispecific” binding agent or antigen binding protein or antibodyis one that targets more than one antigen or epitope.

A “bispecific,” “dual-specific” or “bifunctional” binding agent orantigen binding protein or antibody is a hybrid having two differentantigen binding sites. Biantigen binding proteins, antigen bindingproteins and antibodies are a species of multiantigen binding protein,antigen binding protein or multispecific antibody and may be produced bya variety of methods including, but not limited to, fusion of hybridomasor linking of Fab′ fragments. (See, e.g., Songsivilai and Lachmann,1990, Clin. Exp. Immunol. 79:315-321; Kostelny et al., 1992, J. Immunol.148:1547-1553; Spiess et al., Alternative molecular formats andtherapeutic applications for bispecific antibodies, Mol. Immunol.67:95-106 (2015)). The two binding sites of a bispecific antigen bindingprotein or antibody will bind to two different epitopes, which mayreside on the same or different protein targets.

The term “immunoglobulin” encompasses full antibodies comprising twodimerized heavy chains (HC), each covalently linked to a light chain(LC); a single undimerized immunoglobulin heavy chain and covalentlylinked light chain (HC+LC), or a chimeric immunoglobulin (lightchain+heavy chain)-Fc heterotrimer (a so-called “hemibody”). An“immunoglobulin” is a protein, but is not necessarily an antigen bindingprotein.

In an “antibody”, each tetramer is composed of two identical pairs ofpolypeptide chains, each pair having one “light” chain of about 220amino acids (about 25 kDa) and one “heavy” chain of about 440 aminoacids (about 50-70 kDa). The amino-terminal portion of each chainincludes a “variable” (“V”) region of about 100 to 110 or more aminoacids primarily responsible for antigen recognition. Thecarboxy-terminal portion of each chain defines a constant regionprimarily responsible for effector function. The variable region differsamong different antibodies. The constant region is the same amongdifferent antibodies. Within the variable region of each heavy or lightchain, there are three hypervariable subregions that help determine theantibody's specificity for antigen in the case of an antibody that is anantigen binding protein. However, within the scope of the presentinvention, an embodiment of the immunoglobulin, e.g., an antibody, neednot be an antigen binding protein, or need not be known to specificallybind to an antigen. The variable domain residues between thehypervariable regions are called the framework residues and generallyare somewhat homologous among different antibodies. Immunoglobulins canbe assigned to different classes depending on the amino acid sequence ofthe constant domain of their heavy chains. Human light chains areclassified as kappa (.kappa.) and lambda (.lamda.) light chains. Withinlight and heavy chains, the variable and constant regions are joined bya “J” region of about 12 or more amino acids, with the heavy chain alsoincluding a “D” region of about 10 more amino acids. See generally,Fundamental Immunology, Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y.(1989)). Within the scope of the invention, an “antibody” alsoencompasses a recombinantly made antibody, and antibodies that areglycosylated or lacking glycosylation.

The term “light chain” or “immunoglobulin light chain” includes afull-length light chain and fragments thereof having sufficient variableregion sequence to confer binding specificity. A full-length light chainincludes a variable region domain, V_(L), and a constant region domain,C_(L). The variable region domain of the light chain is at theamino-terminus of the polypeptide. Light chains include kappa chains andlambda chains.

The term “heavy chain” or “immunoglobulin heavy chain” includes afull-length heavy chain and fragments thereof having sufficient variableregion sequence to confer binding specificity. A full-length heavy chainincludes a variable region domain, V_(H), and three constant regiondomains, C_(H1), C_(H2), and C_(H3). The V_(H) domain is at theamino-terminus of the polypeptide, and the C_(H) domains are at thecarboxyl-terminus, with the C_(H3) being closest to the carboxy-terminusof the polypeptide. Heavy chains are classified as mu (μ), delta (δ),gamma (γ), alpha (α), and epsilon (ε), and define the antibody's isotypeas IgM, IgD, IgG, IgA, and IgE, respectively. In separate embodiments ofthe invention, heavy chains may be of any isotype, including IgG(including IgG1, IgG2, IgG3 and IgG4 subtypes), IgA (including IgA1 andIgA2 subtypes), IgM and IgE. Several of these may be further dividedinto subclasses or isotypes, e.g. IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2.Different IgG isotypes may have different effector functions (mediatedby the Fc region), such as antibody-dependent cellular cytotoxicity(ADCC) and complement-dependent cytotoxicity (CDC). In ADCC, the Fcregion of an antibody binds to Fc receptors (Fc.gamma.Rs) on the surfaceof immune effector cells such as natural killers and macrophages,leading to the phagocytosis or lysis of the targeted cells. In CDC, theantibodies kill the targeted cells by triggering the complement cascadeat the cell surface.

An “Fc region”, or used interchangeably herein, “Fc domain” or“immunoglobulin Fc domain”, contains two heavy chain fragments, which ina full antibody comprise the C_(H1) and C_(H2) domains of the antibody.The two heavy chain fragments are held together by two or more disulfidebonds and by hydrophobic interactions of the C_(H3) domains.

The term “salvage receptor binding epitope” refers to an epitope of theFc region of an IgG molecule (e.g., IgG₁, IgG₂, IgG₃, or IgG₄) that isresponsible for increasing the in vivo serum half-life of the IgGmolecule.

In many embodiments of the invention, the protein of interest is anantigen binding protein, such as but not limited to, an antibody,antibody subunit, or antibody fragment. For a detailed description ofthe structure and generation of antibodies, see Roth, D. B., and Craig,N. L., Cell, 94:411-414 (1998), herein incorporated by reference in itsentirety. Briefly, the process for generating DNA encoding the heavy andlight chain immunoglobulin sequences occurs primarily in developingB-cells. Prior to the rearranging and joining of various immunoglobulingene segments, the V, D, J and constant (C) gene segments are foundgenerally in relatively close proximity on a single chromosome. DuringB-cell-differentiation, one of each of the appropriate family members ofthe V, D, J (or only V and J in the case of light chain genes) genesegments are recombined to form functionally rearranged variable regionsof the heavy and light immunoglobulin genes. This gene segmentrearrangement process appears to be sequential. First, heavy chainD-to-J joints are made, followed by heavy chain V-to-DJ joints and lightchain V-to-J joints. In addition to the rearrangement of V, D and Jsegments, further diversity is generated in the primary repertoire ofimmunoglobulin heavy and light chains by way of variable recombinationat the locations where the V and J segments in the light chain arejoined and where the D and J segments of the heavy chain are joined.Such variation in the light chain typically occurs within the last codonof the V gene segment and the first codon of the J segment. Similarimprecision in joining occurs on the heavy chain chromosome between theD and J_(H) segments and may extend over as many as 10 nucleotides.Furthermore, several nucleotides may be inserted between the D and J_(H)and between the V_(H) and D gene segments which are not encoded bygenomic DNA. The addition of these nucleotides is known as N-regiondiversity. The net effect of such rearrangements in the variable regiongene segments and the variable recombination which may occur during suchjoining is the production of a primary antibody repertoire.

The term “hypervariable” region refers to the amino acid residues of anantibody which are responsible for antigen-binding. The hypervariableregion comprises amino acid residues from a complementarity determiningregion or CDR [i.e., residues 24-34 (L1), 50-56 (L2) and 89-97 (L3) inthe light chain variable domain and 31-35 (H1), 50-65 (H2) and 95-102(H3) in the heavy chain variable domain as described by Kabat et al.,Sequences of Proteins of Immunological Interest, th Ed. Public HealthService, National Institutes of Health, Bethesda, Md. (1991)]. Even asingle CDR may recognize and bind antigen, although with a loweraffinity than the entire antigen binding site containing all of theCDRs.

An alternative definition of residues from a hypervariable “loop” isdescribed by Chothia et al., J. Mol. Biol. 196: 901-917 (1987) asresidues 26-32 (L1), 50-52 (L2) and 91-96 (L3) in the light chainvariable domain and 26-32 (H1), 53-55 (H2) and 96-101 (H3) in the heavychain variable domain.

“Framework” or “FR” residues are those variable region residues otherthan the hypervariable region residues.

“Antibody fragments” comprise a portion of an intact full lengthantibody, preferably the antigen binding or variable region of theintact antibody. Examples of antibody fragments include Fab, Fab′,F(ab′)₂, and Fv fragments; diabodies; linear antibodies (Zapata et al.,Protein Eng., 8(10):1057-1062 (1995)); single-chain antibody molecules;and multispecific antibodies formed from antibody fragments.

Papain digestion of antibodies produces two identical antigen-bindingfragments, called “Fab” fragments, each with a single antigen-bindingsite, and a residual “Fc” fragment which contains the constant region.The Fab fragment contains all of the variable domain, as well as theconstant domain of the light chain and the first constant domain (CH1)of the heavy chain. The Fc fragment displays carbohydrates and isresponsible for many antibody effector functions (such as bindingcomplement and cell receptors), that distinguish one class of antibodyfrom another.

Pepsin treatment yields an F(ab′)₂ fragment that has two “Single-chainFv” or “scFv” antibody fragments comprising the V_(H) and V_(L) domainsof antibody, wherein these domains are present in a single polypeptidechain. Fab fragments differ from Fab′ fragments by the inclusion of afew additional residues at the carboxy terminus of the heavy chain CH1domain including one or more cysteines from the antibody hinge region.Preferably, the Fv polypeptide further comprises a polypeptide linkerbetween the VH and VL domains that enables the Fv to form the desiredstructure for antigen binding. For a review of scFv see Pluckthun in ThePharmacology of Monoclonal Antibodies, vol. 1 13, Rosenburg and Mooreeds., Springer-Verlag, New York, pp. 269-315 (1994).

A “Fab fragment” is comprised of one light chain and the C_(H1) andvariable regions of one heavy chain. The heavy chain of a Fab moleculecannot form a disulfide bond with another heavy chain molecule.

A “Fab′ fragment” contains one light chain and a portion of one heavychain that contains the V_(H) domain and the C_(H1) domain and also theregion between the C_(H1) and C_(H2) domains, such that an interchaindisulfide bond can be formed between the two heavy chains of two Fab′fragments to form an F(ab′)₂ molecule.

A “F(ab′)₂ fragment” contains two light chains and two heavy chainscontaining a portion of the constant region between the C_(H1) andC_(H2) domains, such that an interchain disulfide bond is formed betweenthe two heavy chains. A F(ab′)₂ fragment thus is composed of two Fab′fragments that are held together by a disulfide bond between the twoheavy chains.

“Fv” is the minimum antibody fragment that contains a complete antigenrecognition and binding site. This region consists of a dimer of oneheavy- and one light-chain variable domain in tight, non-covalentassociation. It is in this configuration that the three CDRs of eachvariable domain interact to define an antigen binding site on thesurface of the VH VL dimer. A single variable domain (or half of an Fvcomprising only three CDRs specific for an antigen) has the ability torecognize and bind antigen, although at a lower affinity than the entirebinding site.

“Single-chain antibodies” are Fv molecules in which the heavy and lightchain variable regions have been connected by a flexible linker to forma single polypeptide chain, which forms an antigen-binding region.Single chain antibodies are discussed in detail in International PatentApplication Publication No. WO 88/01649 and U.S. Pat. Nos. 4,946,778 and5,260,203, the disclosures of which are incorporated by reference intheir entireties.

“Single-chain Fv” or “scFv” antibody fragments comprise the V_(H) andV_(L) domains of antibody, wherein these domains are present in a singlepolypeptide chain, and optionally comprising a polypeptide linkerbetween the V_(H) and V_(L) domains that enables the Fv to form thedesired structure for antigen binding (Bird et al., Science 242:423-426,1988, and Huston et al., Proc. Nati. Acad. Sci. USA 85:5879-5883, 1988).An “Fd” fragment consists of the V_(H) and C_(H1) domains.

The term “diabodies” refers to small antibody fragments with twoantigen-binding sites, which fragments comprise a heavy-chain variabledomain (V_(H)) connected to a light-chain variable domain (V_(L)) in thesame polypeptide chain (V_(H) V_(L)). By using a linker that is tooshort to allow pairing between the two domains on the same chain, thedomains are forced to pair with the complementary domains of anotherchain and create two antigen-binding sites. Diabodies are described morefully in, for example, EP 404,097; WO 93/11161; and Hollinger et al.,Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993).

A “domain antibody” is an immunologically functional immunoglobulinfragment containing only the variable region of a heavy chain or thevariable region of a light chain. In some instances, two or more V_(H)regions are covalently joined with a peptide linker to create a bivalentdomain antibody. The two V_(H) regions of a bivalent domain antibody maytarget the same or different antigens.

The term “antigen binding protein” (ABP) includes antibodies or antibodyfragments, as defined above, and recombinant peptides or other compoundsthat contain sequences derived from CDRs having the desiredantigen-binding properties such that they specifically bind a targetantigen of interest.

In general, an antigen binding protein, e.g., an antibody or antibodyfragment, “specifically binds” to an antigen of interest when it has asignificantly higher binding affinity for, and consequently is capableof distinguishing, that antigen, compared to its affinity for otherunrelated proteins, under similar binding assay conditions. Typically,an antigen binding protein is said to “specifically bind” its targetantigen when the dissociation constant (K_(D)) is 10⁻⁸ M or lower. Theantigen binding protein specifically binds antigen with “high affinity”when the K_(D) is 10⁻⁹ M or lower, and with “very high affinity” whenthe K_(D) is 10⁻¹⁰ M or lower.

“Antigen binding region” or “antigen binding site” means a portion of aprotein that specifically binds a specified antigen. For example, thatportion of an antigen binding protein that contains the amino acidresidues that interact with an antigen and confer on the antigen bindingprotein its specificity and affinity for the antigen is referred to as“antigen binding region.” An antigen binding region typically includesone or more “complementary binding regions” (“CDRs”). Certain antigenbinding regions also include one or more “framework” regions (“FRs”). A“CDR” is an amino acid sequence that contributes to antigen bindingspecificity and affinity. “Framework” regions can aid in maintaining theproper conformation of the CDRs to promote binding between the antigenbinding region and an antigen. In a traditional antibody, the CDRs areembedded within a framework in the heavy and light chain variable regionwhere they constitute the regions responsible for antigen binding andrecognition. A variable region of an immunoglobulin antigen bindingprotein comprises at least three heavy or light chain CDRs, see, supra(Kabat et al., 1991, Sequences of Proteins of Immunological Interest,Public Health Service N.I.H., Bethesda, Md.; see also Chothia and Lesk,1987, J. Mol. Biol. 196:901-917; Chothia et al., 1989, Nature 342:877-883), within a framework region (designated framework regions 1-4,FR1, FR2, FR3, and FR4, by Kabat et al., 1991, supra; see also Chothiaand Lesk, 1987, supra).

The term “antigen” refers to a molecule or a portion of a moleculecapable of being bound by a selective binding agent, such as an antigenbinding protein (including, e.g., an antibody or immunologicalfunctional fragment thereof), and additionally capable of being used inan animal to produce antibodies capable of binding to that antigen. Anantigen may possess one or more epitopes that are capable of interactingwith different antigen binding proteins, e.g., antibodies.

The term “epitope” is the portion of a molecule that is bound by anantigen binding protein (for example, an antibody). The term includesany determinant capable of specifically binding to an antigen bindingprotein, such as an antibody or to a T-cell receptor. An epitope can becontiguous or non-contiguous (e.g., in a single-chain polypeptide, aminoacid residues that are not contiguous to one another in the polypeptidesequence but that within the context of the molecule are bound by theantigen binding protein). In certain embodiments, epitopes may bemimetic in that they comprise a three dimensional structure that issimilar to an epitope used to generate the antigen binding protein, yetcomprise none or only some of the amino acid residues found in thatepitope used to generate the antigen binding protein. Most often,epitopes reside on proteins, but in some instances may reside on otherkinds of molecules, such as nucleic acids. Epitope determinants mayinclude chemically active surface groupings of molecules such as aminoacids, sugar side chains, phosphoryl or sulfonyl groups, and may havespecific three dimensional structural characteristics, and/or specificcharge characteristics. Generally, antibodies specific for a particulartarget antigen will preferentially recognize an epitope on the targetantigen in a complex mixture of proteins and/or macromolecules.

The term “identity” refers to a relationship between the sequences oftwo or more polypeptide molecules or two or more nucleic acid molecules,as determined by aligning and comparing the sequences. “Percentidentity” means the percent of identical residues between the aminoacids or nucleotides in the compared molecules and is calculated basedon the size of the smallest of the molecules being compared. For thesecalculations, gaps in alignments (if any) must be addressed by aparticular mathematical model or computer program (i.e., an“algorithm”). Methods that can be used to calculate the identity of thealigned nucleic acids or polypeptides include those described inComputational Molecular Biology, (Lesk, A. M., ed.), 1988, New York:Oxford University Press; Biocomputing Informatics and Genome Projects,(Smith, D. W., ed.), 1993, New York: Academic Press; Computer Analysisof Sequence Data, Part I, (Griffin, A. M., and Griffin, H. G., eds.),1994, New Jersey: Humana Press; von Heinje, G., 1987, Sequence Analysisin Molecular Biology, New York: Academic Press; Sequence AnalysisPrimer, (Gribskov, M. and Devereux, J., eds.), 1991, New York: M.Stockton Press; and Carillo et al., 1988, SIAM J. Applied Math. 48:1073.For example, sequence identity can be determined by standard methodsthat are commonly used to compare the similarity in position of theamino acids of two polypeptides. Using a computer program such as BLASTor FASTA, two polypeptide or two polynucleotide sequences are alignedfor optimal matching of their respective residues (either along the fulllength of one or both sequences, or along a pre-determined portion ofone or both sequences). The programs provide a default opening penaltyand a default gap penalty, and a scoring matrix such as PAM 250 [astandard scoring matrix; see Dayhoff et al., in Atlas of ProteinSequence and Structure, vol. 5, supp. 3 (1978)] can be used inconjunction with the computer program. For example, the percent identitycan then be calculated as: the total number of identical matchesmultiplied by 100 and then divided by the sum of the length of thelonger sequence within the matched span and the number of gapsintroduced into the longer sequences in order to align the twosequences. In calculating percent identity, the sequences being comparedare aligned in a way that gives the largest match between the sequences.

The GCG program package is a computer program that can be used todetermine percent identity, which package includes GAP (Devereux et al.,1984, Nucl. Acid Res. 12:387; Genetics Computer Group, University ofWisconsin, Madison, Wis.). The computer algorithm GAP is used to alignthe two polypeptides or two polynucleotides for which the percentsequence identity is to be determined. The sequences are aligned foroptimal matching of their respective amino acid or nucleotide (the“matched span”, as determined by the algorithm). A gap opening penalty(which is calculated as 3.times. the average diagonal, wherein the“average diagonal” is the average of the diagonal of the comparisonmatrix being used; the “diagonal” is the score or number assigned toeach perfect amino acid match by the particular comparison matrix) and agap extension penalty (which is usually 1/10 times the gap openingpenalty), as well as a comparison matrix such as PAM 250 or BLOSUM 62are used in conjunction with the algorithm. In certain embodiments, astandard comparison matrix (see, Dayhoff et al., 1978, Atlas of ProteinSequence and Structure 5:345-352 for the PAM 250 comparison matrix;Henikoff et al., 1992, Proc. Natl. Acad. Sci. U.S.A. 89:10915-10919 forthe BLOSUM 62 comparison matrix) is also used by the algorithm.

Recommended parameters for determining percent identity for polypeptidesor nucleotide sequences using the GAP program include the following:

Algorithm: Needleman et al., 1970, J. Mol. Biol. 48:443-453;

Comparison matrix: BLOSUM 62 from Henikoff et al., 1992, supra;

Gap Penalty: 12 (but with no penalty for end gaps)

Gap Length Penalty: 4

Threshold of Similarity: 0

Certain alignment schemes for aligning two amino acid sequences mayresult in matching of only a short region of the two sequences, and thissmall aligned region may have very high sequence identity even thoughthere is no significant relationship between the two full-lengthsequences. Accordingly, the selected alignment method (GAP program) canbe adjusted if so desired to result in an alignment that spans at least50 contiguous amino acids of the target polypeptide.

The term “modification” when used in connection with proteins ofinterest (e.g., immunoglobulins, including antibodies and antibodyfragments), include, but are not limited to, one or more amino acidchanges (including substitutions, insertions or deletions); chemicalmodifications; covalent modification by conjugation to therapeutic ordiagnostic agents; labeling (e.g., with radionuclides or variousenzymes); covalent polymer attachment such as PEGylation (derivatizationwith polyethylene glycol) and insertion or substitution by chemicalsynthesis of non-natural amino acids. Modified immunoglobulins of theinvention will retain the binding (or non-binding) properties ofunmodified molecules of the invention. By methods known to the skilledartisan, immunoglobulins, such as antibodies, or other proteins, can be“engineered” or modified for improved target affinity, selectivity,stability, and/or manufacturability before the coding sequence of the“engineered” protein is included in the inventive expression cassette.

The term “derivative” when used in connection with proteins of interest,such as immunoglobulins (including antibodies and antibody fragments)refers to proteins that are covalently modified by conjugation totherapeutic or diagnostic agents, labeling (e.g., with radionuclides orvarious enzymes), covalent polymer attachment such as PEGylation(derivatization with polyethylene glycol) and insertion or substitutionby chemical synthesis of non-natural amino acids. Derivatives of theinvention will retain the binding properties of un-derivatizedmolecules.

Within the scope of the invention, proteins of interest can betherapeutic proteins (so-called “biologics.”) The term “therapeuticprotein” means a pharmacologically active protein applicable to theprevention, treatment, or cure of a disease, disorder, or medicalcondition of human beings or other mammals. Examples of therapeuticproteins include, but are not limited to, monoclonal antibodies,recombinant forms of a native protein (e.g., a receptor, ligand,hormone, enzyme or cytokine), fusion proteins, peptibodies, and/or amonomer domain binding proteins, e.g., based on a domain selected fromLDL receptor A-domain, thrombospondin domain, thyroglobulin domain,trefoil/PD domain, VEGF binding domain, EGF domain, Anato domain,Notch/LNR domain, DSL domain, integrin beta domain, and Ca-EGF domain.The preceding are merely exemplary, and a therapeutic protein cancomprise any clinically relevant polypeptide target moiety orpolypeptide ligand.

“Treatment” or “treating” is an intervention performed with theintention of preventing the development or altering the pathology of adisorder. Accordingly, “treatment” refers to both therapeutic treatmentand prophylactic or preventative measures. Those in need of treatmentinclude those already with the disorder as well as those in which thedisorder is to be prevented. “Treatment” includes any indication(s) ofsuccess in the amelioration of an injury, pathology or condition,including any objective or subjective parameter such as abatement;remission; diminishing of symptoms or making the injury, pathology orcondition more tolerable to the patient; slowing in the rate ofdegeneration or decline; making the final point of degeneration lessdebilitating; improving a patient's physical or mental well-being. Thetreatment or amelioration of symptoms can be based on objective orsubjective parameters; including the results of a physical examinationby a physician or other health care provider, self-reporting by apatient, neuropsychiatric exams, and/or a psychiatric evaluation.

An “effective amount” of a therapeutic is generally an amount sufficientto reduce the severity and/or frequency of symptoms, eliminate thesymptoms and/or underlying cause, prevent the occurrence of symptomsand/or their underlying cause, and/or improve or remediate the damagethat results from or is associated with migraine headache. In someembodiments, the effective amount is a therapeutically effective amountor a prophylactically effective amount. A “therapeutically effectiveamount” is an amount sufficient to remedy a disease state (e.g.,transplant rejection or GVHD, inflammation, multiple sclerosis, cancer,cardiovascular disease, diabetes, neuropathy, pain) or symptom(s),particularly a state or symptom(s) associated with the disease state, orotherwise prevent, hinder, retard or reverse the progression of thedisease state or any other undesirable symptom associated with thedisease in any way whatsoever (i.e. that provides “therapeuticefficacy”). A “prophylactically effective amount” is an amount of apharmaceutical composition that, when administered to a subject, willhave the intended prophylactic effect, e.g., preventing or delaying theonset (or reoccurrence) of migraine headache or multiple sclerosissymptoms, or reducing the likelihood of the onset (or reoccurrence) ofmigraine headache, migraine headache symptoms, or multiple sclerosissymptoms. The full therapeutic or prophylactic effect does notnecessarily occur by administration of one dose, and may occur onlyafter administration of a series of doses. Thus, a therapeutically orprophylactically effective amount may be administered in one or moreadministrations.

The protein of interest can be any protein, but in in many embodimentsthe protein is a pharmacologically active protein or peptide.

In some embodiments of the invention, the protein of interest can be amimetic or agonist peptide. The terms “-mimetic peptide,” “peptidemimetic,” and “-agonist peptide” refer to a peptide or protein havingbiological activity comparable to a naturally occurring protein ofinterest. These terms further include peptides that indirectly mimic theactivity of a naturally occurring peptide molecule, such as bypotentiating the effects of the naturally occurring molecule.

In some embodiments of the invention, the protein of interest can be anantagonist peptide or inhibitor peptide. The term “-antagonist peptide,”“peptide antagonist,” and “inhibitor peptide” refer to a peptide thatblocks or in some way interferes with the biological activity of areceptor of interest, or has biological activity comparable to a knownantagonist or inhibitor of a receptor of interest (such as, but notlimited to, an ion channel or a G-Protein Coupled Receptor (GPCR)).

Examples of pharmacologically active proteins that can be used withinthe present invention include, but are not limited to, a toxin peptide,an IL-6 binding peptide, a CD3 binding protein, a CD19 binding protein,a CD20 binding protein, a CD22 binding protein, a HER2 binding protein,a HERS binding protein, a VEGF-A binding protein, a TNF-α bindingprotein, an EGFR binding protein, a RANK ligand binding protein, anIL-1α binding protein, an IL-1β binding protein, an IL-17A bindingprotein, an EPCAM (CD326) binding protein, a CGRP peptide antagonist, abradykinin B1 receptor peptide antagonist, a parathyroid hormone (PTH)agonist peptide, a parathyroid hormone (PTH) antagonist peptide, anang-1 binding peptide, an ang-2 binding peptide, a myostatin bindingpeptide, an erythropoietin-mimetic (EPO-mimetic) peptide, a FGF21peptide, a thrombopoietin-mimetic (TPO-mimetic) peptide (e.g., AMP2 orAMPS), a nerve growth factor (NGF) binding peptide, a B cell activatingfactor (BAFF) binding peptide, and a glucagon-like peptide (GLP)-1 or apeptide mimetic thereof or GLP-2 or a peptide mimetic thereof.

The term peptide or protein “analog” refers to a polypeptide having asequence that differs from a peptide sequence existing in nature by atleast one amino acid residue substitution, internal addition, orinternal deletion of at least one amino acid, and/or amino- orcarboxy-terminal end truncations, or additions). An “internal deletion”refers to absence of an amino acid from a sequence existing in nature ata position other than the N- or C-terminus. Likewise, an “internaladdition” refers to presence of an amino acid in a sequence existing innature at a position other than the N- or C-terminus.

Cloning DNA

Cloning of DNA is carried out using standard techniques (see, e.g.,Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3,Cold Spring Harbor Press, which is incorporated herein by reference).For example, a cDNA library may be constructed by reverse transcriptionof polyA+mRNA, preferably membrane-associated mRNA, and the libraryscreened using probes specific for human immunoglobulin polypeptide genesequences. In one embodiment, however, the polymerase chain reaction(PCR) is used to amplify cDNAs (or portions of full-length cDNAs)encoding an immunoglobulin gene segment of interest (e.g., a light orheavy chain variable segment). The amplified sequences can be readilycloned into any suitable vector, e.g., expression vectors, minigenevectors, or phage display vectors. It will be appreciated that theparticular method of cloning used is not critical, so long as it ispossible to determine the sequence of some portion of the immunoglobulinpolypeptide of interest.

One source for antibody nucleic acids is a hybridoma produced byobtaining a B cell from an animal immunized with the antigen of interestand fusing it to an immortal cell. Alternatively, nucleic acid can beisolated from B cells (or whole spleen) of the immunized animal. Yetanother source of nucleic acids encoding antibodies is a library of suchnucleic acids generated, for example, through phage display technology.Polynucleotides encoding peptides of interest, e.g., variable regionpeptides with desired binding characteristics, can be identified bystandard techniques such as panning.

The sequence encoding an entire variable region of the immunoglobulinpolypeptide may be determined; however, it will sometimes be adequate tosequence only a portion of a variable region, for example, theCDR-encoding portion. Sequencing is carried out using standardtechniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: ALaboratory Guide, Vols 1-3, Cold Spring Harbor Press, and Sanger, F. etal. (1977) Proc. Natl. Acad. Sci. USA 74: 5463-5467, which isincorporated herein by reference). By comparing the sequence of thecloned nucleic acid with published sequences of human immunoglobulingenes and cDNAs, one of skill will readily be able to determine,depending on the region sequenced, (i) the germline segment usage of thehybridoma immunoglobulin polypeptide (including the isotype of the heavychain) and (ii) the sequence of the heavy and light chain variableregions, including sequences resulting from N-region addition and theprocess of somatic mutation. One source of immunoglobulin gene sequenceinformation is the National Center for Biotechnology Information,National Library of Medicine, National Institutes of Health, Bethesda,Md.

Isolated DNA can be operably linked to control sequences or placed intoexpression vectors, which are then transfected into host cells that donot otherwise produce immunoglobulin protein, to direct the synthesis ofmonoclonal antibodies in the recombinant host cells. Recombinantproduction of antibodies is well known in the art.

Nucleic acid is operably linked when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for apresequence or secretory leader is operably linked to DNA for apolypeptide if it is expressed as a preprotein that participates in thesecretion of the polypeptide; a promoter or enhancer is operably linkedto a coding sequence if it affects the transcription of the sequence; ora ribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, operably linkedmeans that the DNA sequences being linked are contiguous, and, in thecase of a secretory leader, contiguous and in reading phase. However,enhancers do not have to be contiguous. Linking is accomplished byligation at convenient restriction sites. If such sites do not exist,the synthetic oligonucleotide adaptors or linkers are used in accordancewith conventional practice.

Many vectors are known in the art. Vector components may include one ormore of the following: a signal sequence (that may, for example, directsecretion of the antibody; e.g.,ATGGACATGAGGGTGCCCGCTCAGCTCCTGGGGCTCCTGCTGCTGTGGCTGAGAG GTGCGCGCTGT//SEQ ID NO:7, which encodes the VK-1 signal peptide sequenceMDMRVPAQLLGLLLLWLRGARC//SEQ ID NO:8), an origin of replication, one ormore selective marker genes (that may, for example, confer antibiotic orother drug resistance, complement auxotrophic deficiencies, or supplycritical nutrients not available in the medium), an enhancer element, apromoter, and a transcription termination sequence, all of which arewell known in the art.

By way of further illustration, the following numbered embodiments areencompassed by the present invention:

Embodiment 1: A hybrid promoter (or control sequence) comprising:

-   -   (i) a mCMV enhancer sequence, comprising a mCMV enhancer element        (mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end,        operably linked 5′ to a rat EF-1alpha intron sequence;    -   (ii) an intervening first leader sequence operably linked, 3′ to        the CMV promoter sequence of the mCMV enhancer sequence, and 5′        to the rat EF-1alpha intron sequence; and    -   (iii) a second leader sequence operably linked 3′ to the rat        EF-1alpha intron sequence.

Embodiment 2: The hybrid promoter of Embodiment 1, wherein the CMVpromoter sequence at the 3′ end of the mCMV enhancer sequence comprisesa segment having the nucleotide sequence of SEQ ID NO:24 or SEQ IDNO:26.

Embodiment 3: The hybrid promoter of any of Embodiments 1-2, wherein therat EF-1alpha intron sequence comprises the nucleotide sequence of SEQID NO:4.

Embodiment 4: The hybrid promoter of any of Embodiments 1-3, wherein themCMV enhancer sequence comprises the nucleotide sequence of SEQ ID NO:2or SEQ ID NO:33; and the rat EF-1alpha intron sequence comprises thenucleotide sequence of SEQ ID NO:4.

Embodiment 5: The hybrid promoter of any of Embodiments 1-4, wherein thefirst leader sequence comprises the nucleotide sequence of SEQ ID NO:3.

Embodiment 6: The hybrid promoter of any of Embodiments 1-5, wherein thesecond leader sequence comprises the nucleotide sequence of SEQ ID NO:5.

Embodiment 7: The hybrid promoter of any of Embodiments 1-6, furthercomprising one or more TetO sequences inserted within the CMV promotersequence.

Embodiment 8: The hybrid promoter of any of Embodiments 1-7, comprisinga nucleotide sequence having at least 95% sequence identity to thenucleotide sequence of any of SEQ ID NO:1, SEQ ID NO:30, SEQ ID NO:31,or SEQ ID NO:32.

Embodiment 9: An expression cassette, comprising:

-   -   the hybrid promoter (or control sequence) of any of Embodiments        1-8, operably linked 5′ to an open reading frame encoding an        exogenous protein of interest; and a polyadenylation site        operably linked 3′ to the open reading frame.

Embodiment 10: A recombinant expression vector comprising the expressioncassette of Embodiment 9.

Embodiment 11: A mammalian host cell comprising the recombinantexpression vector of Embodiment 10.

Embodiment 12: The mammalian host cell of Embodiment 11, further beingcapable of expressing TetR.

Embodiment 13: The mammalian host cell of any of Embodiments 11-12,being derived from a Chinese Hamster Ovary (CHO) cell.

Embodiment 14: The mammalian host cell of any of Embodiments 11-13,selected from the group consisting of a CHO-K1 cell, a DXB11 cell, and aDG44 cell.

Embodiment 15: A method of producing a protein of interest, comprising:

-   -   (a) culturing the mammalian host cell of any of Embodiments        11-14, in an aqueous medium under physiological conditions        permitting expression of the protein of interest; and    -   (b) recovering the protein of interest from the medium.

Embodiment 16: A method of producing a protein of interest, comprising:

-   -   (a) culturing a mammalian host cell that comprises an expression        vector comprising the hybrid promoter (or control sequence) of        any of Embodiments 7-8, in an aqueous medium under physiological        conditions, wherein the mammalian host cell is capable of        expressing TetR, whereby, in the absence of tetracycline in the        medium, the expression of the protein of interest is repressed;    -   (b) adding tetracycline to the aqueous medium in an amount        sufficient to bind TetR in the host cell, whereby expression of        the protein of interest by the host cell is derepressed; and    -   (c) recovering the protein of interest from the medium.

Embodiment 17: The method of any of Embodiments 15-16, wherein theaqueous medium is serum-free.

Embodiment 18: The method of any of Embodiments 15-16, wherein culturingthe mammalian host cell is in a suspension in liquid aqueous medium.

Embodiment 19: The method of any of Embodiments 15-16, wherein culturingthe mammalian host cell is in an adhesion layer on a solid or semisolidsubstrate.

Embodiment 20: A recombinant expression vector, comprising:

-   -   (a) a 5′ PiggyBac ITR comprising the nucleotide sequence of SEQ        ID NO:45;    -   (b) a first expression cassette, comprising:        -   (i) a control sequence comprising:            -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer                element (mCMV-E) and a CMV promoter (CMV-P) sequence at                its 3′ end, operably linked 5′ to a rat EF-1alpha intron                sequence;            -   (2) an intervening first leader sequence operably                linked, 3′ to the CMV-P sequence of the mCMV enhancer                sequence, and 5′ to the rat EF-1alpha intron sequence;                and            -   (3) a second leader sequence operably linked 3′ to the                rat EF-1alpha intron sequence;        -   (ii) an open reading frame encoding a protein of interest            operably linked to the control sequence; and        -   (iii) a polyadenylation site operably linked 3′ to the open            reading frame;    -   (c) a second expression cassette, comprising:        -   (i) a weak constitutive promoter, operably linked to an open            reading frame encoding a selectable marker; and        -   (ii) a polyadenylation site operably linked 3′ to the open            reading frame; and    -   (d) a 3′ PiggyBac ITR comprising the nucleotide sequence of SEQ        ID NO:47.

Embodiment 21: The vector of Embodiment 20, further comprising:

-   -   (e) a third expression cassette comprising:        -   (i) a control sequence comprising a promoter;        -   (ii) an open reading frame encoding a protein of interest            (different or the same as the protein of interest encoded by            the open reading frame of the first expression cassette)            operably linked to the control sequence; and        -   (iii) a second polyadenylation site operably linked 3′ to            the open reading frame.

Embodiment 22: The vector of Embodiment 21, wherein the control sequence(i) of the third expression cassette comprises:

-   -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer element        (mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end,        operably linked 5′ to a rat EF-1alpha intron sequence;    -   (2) an intervening first leader sequence operably linked, 3′ to        the CMV-P sequence of the mCMV enhancer sequence, and 5′ to the        rat EF-1alpha intron sequence; and    -   (3) a second leader sequence operably linked 3′ to the rat        EF-1alpha intron sequence.

Embodiment 23: The recombinant expression vector of any of Embodiments20-22, wherein the weak constitutive promoter is a deleted SV40promoter.

Embodiment 24: The recombinant expression vector of any of Embodiments20-23, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:53.

Embodiment 25: The recombinant expression vector of any of Embodiments20-24, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:46.

Embodiment 26: The recombinant expression vector of any of Embodiments20-25, wherein the selectable marker is glutamine synthetase, puromycinresistance, neomycin resistance, zeomycin resistance, or dihydrofolatereductase.

Embodiment 27: The recombinant expression vector of any of Embodiments20-26, wherein the selectable marker is glutamine synthetase.

Embodiment 28: The recombinant expression vector of any of Embodiments20-27, wherein the selectable marker is encoded by the nucleotidesequence of SEQ ID NO:49, or a degenerate DNA sequence.

Embodiment 29: A recombinant expression vector, comprising:

-   (a) a first expression cassette, comprising:    -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding a first immunoglobulin        subunit operably linked to the control sequence; and    -   (iii) a first polyadenylation site operably linked 3′ to the        open reading frame;-   (b) a second expression cassette 3′ to the first expression    cassette, comprising:    -   (i) a control sequence comprising a promoter;    -   (ii) an open reading frame encoding a second immunoglobulin        subunit operably linked to the promoter; and    -   (iii) a second polyadenylation site operably linked 3′ to the        open reading frame; and-   (c) a transcription termination sequence 3′ to the first expression    cassette and 5′ to the second expression cassette.

Embodiment 30: The vector of Embodiment 29, wherein the control sequence(i) of the second expression cassette comprises:

(1) a mCMV enhancer sequence, comprising a mCMV enhancer element(mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end, operablylinked 5′ to a rat EF-1alpha intron sequence;

(2) an intervening first leader sequence operably linked, 3′ to theCMV-P sequence of the mCMV enhancer sequence, and 5′ to the ratEF-1alpha intron sequence; and

(3) a second leader sequence operably linked 3′ to the rat EF-1alphaintron sequence.

Embodiment 31: The vector of any of Embodiments 29-30, furthercomprising:

-   (d) a third expression cassette comprising:-   (i) a weak constitutive promoter, operably linked to an open reading    frame encoding a selectable marker; and-   (ii) a polyadenylation site operably linked 3′ to the open reading    frame.

Embodiment 32: The vector of Embodiment 31, wherein the weakconstitutive promoter is a deleted SV40 promoter.

Embodiment 33: The vector of Embodiment 32, wherein the deleted SV40promoter comprises the nucleotide sequence of SEQ ID NO:53.

Embodiment 34: The vector of any of Embodiments 32-33, wherein thedeleted SV40 promoter comprises the nucleotide sequence of SEQ ID NO:46.

Embodiment 35: The vector of any of Embodiments 31-34, wherein theselectable marker is glutamine synthetase, puromycin resistance,neomycin resistance, zeomycin resistance, or dihydrofolate reductase.

Embodiment 36: The vector of any of Embodiments 31-35, wherein theselectable marker is glutamine synthetase.

Embodiment 37: The vector of any of Embodiments 31-36, wherein theselectable marker is encoded by the nucleotide sequence of SEQ ID NO:49,or a degenerate DNA sequence.

Embodiment 38: A mammalian host cell, comprising the recombinantexpression vector of any of Embodiments 20-37.

Embodiment 39: The mammalian host cell of Embodiment 38, wherein themammalian host cell is a CHO cell.

Embodiment 40: The mammalian host cell of Embodiment 39, wherein the CHOcell is a CHO-K1 cell, a DXB11 cell, or a DG44 cell.

Embodiment 41: A method of producing a protein of interest, in vitro,comprising culturing the mammalian host cell of any of Embodiments 38-40in an aqueous medium under physiological conditions permittingexpression of the protein of interest; and recovering the protein ofinterest from the medium.

Embodiment 42: A recombinant expression vector, comprising:

(a) a 5′ PiggyBac ITR comprising the nucleotide sequence of SEQ IDNO:45;(b) a first expression cassette, comprising:

-   -   (i) a control sequence comprising:        -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer            element (mCMV-E) and a CMV promoter (CMV-P) sequence at its            3′ end, operably linked 5′ to a rat EF-1alpha intron            sequence, comprising one or more TetO sequences inserted            within the CMV-P sequence;        -   (2) an intervening first leader sequence operably linked, 3′            to the CMV-P sequence of the mCMV enhancer sequence, and 5′            to the rat EF-1alpha intron sequence; and        -   (3) a second leader sequence operably linked 3′ to the rat            EF-1alpha intron sequence;    -   (ii) an open reading frame encoding a protein of interest        operably linked to the control sequence; and    -   (iii) a polyadenylation site operably linked 3′ to the open        reading frame;        (c) a second expression cassette, comprising:    -   (i) a weak constitutive promoter, operably linked to an open        reading frame encoding a selectable marker; and    -   (ii) a polyadenylation site operably linked 3′ to the open        reading frame; and        (d) a 3′ PiggyBac ITR comprising the nucleotide sequence of SEQ        ID NO:47.

Embodiment 43: The recombinant expression vector of Embodiment 42,further comprising:

(e) a third expression cassette comprising:

-   -   (i) a control sequence comprising an inducible promoter        comprising one or more TetO sequences;    -   (ii) an open reading frame encoding a protein of interest        (different or the same as the protein of interest encoded by the        open reading frame of the first expression cassette) operably        linked to the control sequence; and    -   (iii) a second polyadenylation site operably linked 3′ to the        open reading frame.

Embodiment 44: The recombinant expression vector of Embodiment 43,wherein the control sequence (i) of the third expression cassettecomprises:

(1) a mCMV enhancer sequence, comprising a mCMV enhancer element(mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end, operablylinked 5′ to a rat EF-1alpha intron sequence, comprising one or moreTetO sequences inserted within the CMV-P sequence;

(2) an intervening first leader sequence operably linked, 3′ to theCMV-P sequence of the mCMV enhancer sequence, and 5′ to the ratEF-1alpha intron sequence; and

(3) a second leader sequence operably linked 3′ to the rat EF-1alphaintron sequence.

Embodiment 45: The recombinant expression vector of any of Embodiments42-44, wherein the weak constitutive promoter is a deleted SV40promoter.

Embodiment 46: The recombinant expression vector of any of Embodiments42-45, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:53.

Embodiment 47: The recombinant expression vector of any of Embodiments42-46, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:46.

Embodiment 48: The recombinant expression vector of any of Embodiments42-47, wherein the selectable marker is glutamine synthetase, puromycinresistance, neomycin resistance, zeomycin resistance, or dihydrofolatereductase.

Embodiment 49: The recombinant expression vector of any of Embodiments42-48, wherein the selectable marker is glutamine synthetase.

Embodiment 50: The recombinant expression vector of any of Embodiments42-49, wherein the selectable marker is encoded by the nucleotidesequence of SEQ ID NO:49, or a degenerate DNA sequence.

Embodiment 51: A method of selecting a stable production cell line formanufacturing a protein of interest, comprising the following steps:

(a) culturing a mammalian host cell stably transfected with therecombinant expression vector of any of Embodiments 42-44, underselective pressure with respect to a selectable marker constitutivelyexpressed from the weak constitutive promoter, in an aqueous mediumunder physiological conditions, wherein the mammalian host cell iscapable of expressing TetR, in the absence of tetracycline or atetracycline analog in the medium, whereby expression of protein fromthe first expression cassette and, if present in the vector, from thethird expression cassette, is repressed;

(b) selecting a viable cell line from the host cell(s) cultured in step(a);

(c) culturing the viable cell line from step (b) in an aqueous mediumcontaining tetracycline or a tetracycline analog in an amount sufficientto bind TetR in the host cell(s), whereby expression of the protein ofinterest by the host cell is derepressed; and

(d) detecting the protein of interest in the culture medium;

(e) selecting a stable production cell line from step (c) that producesa greater amount of the protein of interest relative to a controltransfectant in which the aqueous medium in steps (a) and (c) containedtetracycline or a tetracycline analog in an amount sufficient to bindTetR in the host cell, whereby the expression of the protein of interestwas derepressed in the control transfectant.

Embodiment 52: The method of Embodiment 51, wherein the mammalian hostcell is a CHO cell.

Embodiment 53: The method of any of Embodiments 51-52, wherein the CHOcell is a CHO-K1 cell, a DXB11 cell, or a DG44 cell.

Embodiment 54: A recombinant expression vector, comprising:

(a) a first expression cassette, comprising:

(i) a control sequence comprising:

-   -   (1) a mCMV enhancer sequence, comprising a mCMV enhancer element        (mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end,        operably linked 5′ to a rat EF-1alpha intron sequence,        comprising one or more TetO sequences inserted within the CMV-P        sequence;    -   (2) an intervening first leader sequence operably linked, 3′ to        the CMV-P sequence of the mCMV enhancer sequence, and 5′ to the        rat EF-1alpha intron sequence; and    -   (3) a second leader sequence operably linked 3′ to the rat        EF-1alpha intron sequence;

(ii) an open reading frame encoding a first immunoglobulin subunitoperably linked to the control sequence; and

(iii) a first polyadenylation site operably linked 3′ to the openreading frame;

(b) a second expression cassette 3′ to the first expression cassette,comprising:

(i) a control sequence comprising a promoter;

(ii) an open reading frame encoding a second immunoglobulin subunitoperably linked to the promoter; and

(iii) a second polyadenylation site operably linked 3′ to the openreading frame; and

(c) a transcription termination sequence 3′ to the first expressioncassette and 5′ to the second expression cassette.

Embodiment 55: The recombinant expression vector of Embodiment 54,wherein the control sequence (i) of the second expression cassettecomprises:

(1) a mCMV enhancer sequence, comprising a mCMV enhancer element(mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′ end, operablylinked 5′ to a rat EF-1 alpha intron sequence, comprising one or moreTetO sequences inserted within the CMV-P sequence;

(2) an intervening first leader sequence operably linked, 3′ to theCMV-P sequence of the mCMV enhancer sequence, and 5′ to the ratEF-1alpha intron sequence; and

(3) a second leader sequence operably linked 3′ to the rat EF-1alphaintron sequence.

Embodiment 56: The recombinant expression vector of any of Embodiments54-55, further comprising:

(d) a third expression cassette comprising:

-   -   (i) a weak constitutive promoter, operably linked to an open        reading frame encoding a selectable marker; and    -   (ii) a polyadenylation site operably linked 3′ to the open        reading frame.

Embodiment 57: The recombinant expression vector of Embodiment 56,wherein the weak constitutive promoter is a deleted SV40 promoter.

Embodiment 58: The recombinant expression vector of any of Embodiments56-57, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:53.

Embodiment 59: The recombinant expression vector of any of Embodiments56-58, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:46.

Embodiment 60: The recombinant expression vector of any of Embodiments56-59, wherein the selectable marker is glutamine synthetase, puromycinresistance, neomycin resistance, zeomycin resistance, or dihydrofolatereductase.

Embodiment 61: The recombinant expression vector of any of Embodiments56-60, wherein the selectable marker is glutamine synthetase.

Embodiment 62: The recombinant expression vector of any of Embodiments56-61, wherein the selectable marker is encoded by the nucleotidesequence of SEQ ID NO:49, or a degenerate DNA sequence.

Embodiment 63: A mammalian host cell, comprising the recombinantexpression vector of any of Embodiments 42-50 and 54-62.

Embodiment 64: The mammalian host cell of Embodiment 63, wherein themammalian host cell is a CHO cell.

Embodiment 65: The mammalian host cell of Embodiment 64, wherein the CHOcell is a CHO-K1 cell, a DXB11 cell, or a DG44 cell.

Embodiment 66: A method of producing a protein of interest, in vitro,comprising culturing the mammalian host cell of any of Embodiments 63-65in an aqueous medium under physiological conditions permittingexpression of the protein of interest; and recovering the protein ofinterest from the medium.

The following working examples are illustrative and not to be construedin any way as limiting the scope of the invention.

EXAMPLES Example 1. Materials and Methods

Vector construction. All vectors C, D, E, F, and G included a DNAsequence encoding an exogenous protein of interest “Fc-A” (or “FC-A”; anexemplary Fc fusion with a therapeutic anti-inflammatory antibody), anIRES derived from EMCV virus, the murine dihydrofolate reductase gene,and a 221-bp late polyadenylation derived from SV40 virus as describedpreviously (Kaufman, R. J. et al., “Improved vectors for stableexpression of foreign genes in mammalian cells by use of theuntranslated leader sequence from EMC virus”, Nucl. Acids Res. 19(16):4485-4490 (1991); Schek, et al., “Definition of the upstream efficiencyelement of the simian virus 40 late polyadenylation signal by using invitro analyses”, Mol. Cell. Biol. 12(12):5386-93 (1992)). The junctionbetween the IRES and DHFR was aaaaacacgatTGCTCGAGAGTTGCCACCCATCatg//SEQID NO:6, where the lower case letters represent the endogenous IRESsequence and the ATG transcription start site of DHFR is italicizedlower case. A single transcript is initiated from these variousconstructs, which then includes the Fc-A gene, the EMCV IRES, the murineDHFR gene and terminates at the SV40 polyadenylation site.

Various transcription promoting sequences were included either 5′ orboth 5′ and 3′ to the sequence described above. This allowed allplasmids to be selected using the DHFR gene and Fc-A as a marker forrelative expression. The plasmid backbone for all plasmids waspUC57-simple Genscript (Piscataway, N.J.).

Several exemplary plasmids are represented schematically in FIG. 1.Vector C contained the human CMV and human EF-1alpha intron sequencesdescribed previously (Kim, Lee, Shin, Kang, & Kim, 2002). Vector F(FIG. 1) contained sequences flanking the endogenous Chinese hamsterovary (CHO) EF-1alpha gene as described (Running Deer, J., & Allison, D.S., High-level expression of proteins in mammalian cells usingTranscription Regulatory sequences from Chinese Hamster Ovary EF-1alphaGene, Biotechnology Progress 20:880-889 (2004)) with 4083 bp 5′sequences flanking the ATG and 4174 bp 3′ flanking sequences followingthe polyadenylation site. Vector G (FIG. 1) was constructed by deletinga 240 bp sequence from the transcription start site of the CHO EF-1alphagene to the FSEI site and replacing it with a DNA fragment encompassingthe murine CMV fragment from position −615 to the transcriptional startsite. Vector D (FIG. 1) was constructed by synthesizing the fragmentshown in SEQ ID NO:1 (containing murine CMV GenBank: L06816.1,nucleotides 4067-4682, Rat EF-1alpha intron Genbank: AC158987.3,nucleotides 22137-21728) and placing these sequences 5′ of the Fc-Acoding sequence. Vector C and Vector D also contained the adenovirustripartite leader that replaces the endogenous 3′ untranslated leadersequence (Kaufman et al., 1991). The pUC57-simple vector is not shown inFIG. 1. The complete map of Vector D is shown in FIG. 2.

Electroporation and culture of cells. Long duration electroporation wereperformed as described previously (Bodwell, et al., “Long Durationelectroporation for achieving high level expression of glucocorticoireceptors n mammalian cell lines”, J. Steriod Biochem. and Mol. Biol.,68(e 8), 77-82 (1999)). Briefly, 2×10⁷ cells were resuspended in 0.3 mLof HBS buffer (0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% v/vPolysorbate20), 25 mg of DNA was added, and electroporated in a 4 mm gapcuvette using a BTX EM 600 with a capacitance of 3175 μF, 720 ohms, and200 volts.

DXB11 and DG44 cells were cultured in either PowerCHO2 (Lonza), ProCHO4(Lonza) or Ex-cell 302 (Sigma) according to the manufacturer'sinstructions. Cells were cultured every 3-4 days and seeded at 4×10⁵cells/ml for a 3-day culture or 3×10⁵ cells/ml for a 4-day culture.

Protein titer was determined by affinity High Performance LiquidChromatography (HPLC) using POROS A/20 Protein A column.

Example 2. Transfection of CHO Cells

CHO cells were transfected with various constructs expressing the Fc-Afusion protein. These constructs are shown in FIG. 1 and FIG. 2.Transfected pools of cells were compared for their expression of Fc-Afusion protein.

Transfection of DXB11 cells. The various Fc-A expression plasmids wereused to transfect DXB11, a DHFR mutant CHO cell line, usingelectroporation. These cells were grown in ProCHO4 and were firstselected for growth in culture medium lacking hypoxanthine and thymidineand then selected at 150 nM methotrexate (MTX). Pools of cells selectedwith 150 nM MTX were seeded at 1×10⁶ cells/ml and fed Ex-cell AdvancedCHO Feed 1 (SAFC) and glucose on days 2, 4 and 7. Supernatant fluid washarvested on day 8 and analyzed by poros protein A as described above.

The Fc-A protein titer and specific productivity (picograms per cell perday) are shown in FIG. 3A and FIG. 3B, respectively. The resultsdemonstrated that the hybrid promoter containing murine CMV enhancercombined with the rat EF-1alpha intron and suitable leader sequences(e.g., here the adenovirus tripartite leader; vector D), enhancedexpression of the Fc-A recombinant protein by pools of transfectedcells. The protein titers achieved were superior to other constructs andspecific productivity was as good or better than that obtained usingother constructs.

Transfection of DXB-11 with Vectors D, F, and G. Vectors D, F, and G(FIG. 1) were used to transfect DXB11 cells growing in PowerCHO2. Cellswere first selected for the growth in medium lacking hypoxanthine andthymidine, amplified to 150 nM MTX and then re-amplified to 500 nM MTXto further enhance expression. These pools were seeded at 1×10⁶ cells/mland fed with Ex-cell Advanced CHO Feed 1 and glucose on days 2, 3 and 6.Supernatant fluid was harvested on day 8. As shown in FIG. 4A and FIG.4B, respectively, the titer of those pools transfected with Vector Dwere significantly higher compared to Vectors F and G. The specificproductivities of Vector D were generally higher than Vector F and G.

Transfection of DG44 and DXB-11 with Vectors D and F. CHO cells weretransfected with Vectors D and F expressing Fc-A fusion protein. DXB11cells growing in Ex-cell 302 were transfected as described above. DG44,another DHFR mutant cell line, was grown in PowerCHO2 and transfectedidentically to the DXB11 cells. Transfected pools of cells were comparedfor their expression of Fc-A. Cells were transfected usingelectroporation, selected for growth in culture medium lackinghypoxanthine and thymidine, and then amplified to 150 nM MTX. The DXB11were further amplified to 500 nM MTX and the DG44 cells were furtheramplified to 1 uM MTX. Pools of cells were then seeded by a 1:5 dilutioninto growth medium supplemented with Ex-cell Advanced CHO Feed 1, fed ondays 3, 6 and 8 with Ex-cell Advanced CHO Feed 1 and glucose.Supernatant fluid was harvested on day 10 and analyzed by poros proteinA as described above. The titer and specific productivity are shown inFIG. 5A and FIG. 5B, respectively.

DXB11 Pools transfected with Vector D expressed nearly twice as muchFc-A fusion protein as those pools transfected with Vector F. Pools ofDG44 cells transfected with Vectors D and F expressed at similar levels.However, the pools transfected with the Vector D had slightly higherspecific productivity. The lower specific productivity of DG44 cellscompared to DXB11 cells implies that DG44 cells are less sensitive tothe MTX than DXB11 cells.

Vector D also included a 5′ untranslated (5′UTR) leader sequence derivedfrom adenovirus tripartite leader (TPL). The TPL has been shown toenhance expression of proteins under stress conditions (Logan & Shenk,“Adenovirus tripartite leader sequence enhances translation of mRNAslate after infection”, Proc. Natl. Acad. Sci. USA 81(12): 3655-59(1984)). Whether the TPL is enhancing expression in these studies isunclear, but other studies have shown that the exact nucleotidesequences of the 5′UTR that one may use in this position varies as long,as they do not contain extensive secondary structures or initiatorcodons prior to the authentic initiator codon (Mignone, F. et al.,Untranslated regions of mRNAs. Genome Biology,3(3):reviews0004.1-0004.10 (2002)).

Example 3. Tetracycline-Inducible Expression from the Inventive HybridPromoter (Control Sequence)

In cells expressing the Tet repressor (TetR), tetracycline can be usedto regulate expression from promoters containing the Tet operatorsequence (Yao et al.). Introduction of the Tet operator (TetO) sequencejust 3′ of the TATA box prevents transcription from this promoter in thepresence of the TetR. Presumably, TetR binds to TetO and preventstranscription factors from interacting with the transcription start siteor interfere with the transcription initiation complex formation (Yao etal). Notably, positioning of the TetO sequences is critical indetermining if TetR can effectively modulate transcription. (See, Yao etal., Tetracycline repressor, tetR, rather than the tetR-mammalian celltranscription factor fusion derivatives, regulates inducible geneexpression in mammalian cells, Hum. Gene Ther. 9(13):1939-50 (1998)).

Yao et al. hypothesized that positioning the TetO sequence 10 bpdownstream of the TATATAA sequence allows binding of the TetR to thesame surface as the TATA binding protein. Consistent with thishypothesis, Kim et al. found that insertion of TetO sequences atposition 0 or 15 downstream of the hCMV US11 TATAAG sequence failed topreserve repression in the presence of TetR. (See, Kim et al.,“Tetracycline repressor-regulated gene repression in recombinant humancytomegalovirus”, J. Virol. 69: 2565-257 (1995)).

Tetracycline (Tet), when added to the culture, will bind TetR andinhibit binding to the TetO sequence, thus allowing transcription. Tocreate a powerful Tet-regulated promoter based on the inventive mCMVenhancer sequence/rat EF-1a intron hybrid promoter sequences, we firstgenerated a plasmid driving LacZ (beta-galactosidase protein)expression, JV56_pJV39_pJV10_pUC57S (herein abbreviated as “pJV56”; FIG.6). The LacZ open reading frame is SEQ ID NO:12:

SEQ ID NO: 12 ATGGGGGGTTCTCATCATCATCATCATCATGGTATGGCTAGCATGACTGGTGGACAGCAAATGGGTCGGGATCTGTACGACGATGACGATAAGGTACCTAAGGATCAGCTTGGAGTTGATCCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTAACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTAACTCGGCGTTTCATCTGTGGTGCAACGGGCGCTGGGTCGGTTACGGCCAGGACAGTCGTTTGCCGTCTGAATTTGACCTGAGCGCATTTTTACGCGCCGGAGAAAACCGCCTCGCGGTGATGGTGCTGCGTTGGAGTGACGGCAGTTATCTGGAAGATCAGGATATGTGGCGGATGAGCGGCATTTTCCGTGACGTCTCGTTGCTGCATAAACCGACTACACAAATCAGCGATTTCCATGTTGCCACTCGCTTTAATGATGATTTCAGCCGCGCTGTACTGGAGGCTGAAGTTCAGATGTGCGGCGAGTTGCGTGACTACCTACGGGTAACAGTTTCTTTATGGCAGGGTGAAACGCAGGTCGCCAGCGGCACCGCGCCTTTCGGCGGTGAAATTATCGATGAGCGTGGTGGTTATGCCGATCGCGTCACACTACGTCTGAACGTCGAAAACCCGAAACTGTGGAGCGCCGAAATCCCGAATCTCTATCGTGCGGTGGTTGAACTGCACACCGCCGACGGCACGCTGATTGAAGCAGAAGCCTGCGATGTCGGTTTCCGCGAGGTGCGGATTGAAAATGGTCTGCTGCTGCTGAACGGCAAGCCGTTGCTGATTCGAGGCGTTAACCGTCACGAGCATCATCCTCTGCATGGTCAGGTCATGGATGAGCAGACGATGGTGCAGGATATCCTGCTGATGAAGCAGAACAACTTTAACGCCGTGCGCTGTTCGCATTATCCGAACCATCCGCTGTGGTACACGCTGTGCGACCGCTACGGCCTGTATGTGGTGGATGAAGCCAATATTGAAACCCACGGCATGGTGCCAATGAATCGTCTGACCGATGATCCGCGCTGGCTACCGGCGATGAGCGAACGCGTAACGCGAATGGTGCAGCGCGATCGTAATCACCCGAGTGTGATCATCTGGTCGCTGGGGAATGAATCAGGCCACGGCGCTAATCACGACGCGCTGTATCGCTGGATCAAATCTGTCGATCCTTCCCGCCCGGTGCAGTATGAAGGCGGCGGAGCCGACACCACGGCCACCGATATTATTTGCCCGATGTACGCGCGCGTGGATGAAGACCAGCCCTTCCCGGCTGTGCCGAAATGGTCCATCAAAAAATGGCTTTCGCTACCTGGAGAGACGCGCCCGCTGATCCTTTGCGAATACGCCCACGCGATGGGTAACAGTCTTGGCGGTTTCGCTAAATACTGGCAGGCGTTTCGTCAGTATCCCCGTTTACAGGGCGGCTTCGTCTGGGACTGGGTGGATCAGTCGCTGATTAAATATGATGAAAACGGCAACCCGTGGTCGGCTTACGGCGGTGATTTTGGCGATACGCCGAACGATCGCCAGTTCTGTATGAACGGTCTGGTCTTTGCCGACCGCACGCCGCATCCAGCGCTGACGGAAGCAAAACACCAGCAGCAGTTTTTCCAGTTCCGTTTATCCGGGCAAACCATCGAAGTGACCAGCGAATACCTGTTCCGTCATAGCGATAACGAGCTCCTGCACTGGATGGTGGCGCTGGATGGTAAGCCGCTGGCAAGCGGTGAAGTGCCTCTGGATGTCGCTCCACAAGGTAAACAGTTGATTGAACTGCCTGAACTACCGCAGCCGGAGAGCGCCGGGCAACTCTGGCTCACAGTACGCGTAGTGCAACCGAACGCGACCGCATGGTCAGAAGCCGGGCACATCAGCGCCTGGCAGCAGTGGCGTCTGGCGGAAAACCTCAGTGTGACGCTCCCCGCCGCGTCCCACGCCATCCCGCATCTGACCACCAGCGAAATGGATTTTTGCATCGAGCTGGGTAATAAGCGTTGGCAATTTAACCGCCAGTCAGGCTTTCTTTCACAGATGTGGATTGGCGATAAAAAACAACTGCTGACGCCGCTGCGCGATCAGTTCACCCGTGCACCGCTGGATAACGACATTGGCGTAAGTGAAGCGACCCGCATTGACCCTAACGCCTGGGTCGAACGCTGGAAGGCGGCGGGCCATTACCAGGCCGAAGCAGCGTTGTTGCAGTGCACGGCAGATACACTTGCTGATGCGGTGCTGATTACGACCGCTCACGCGTGGCAGCATCAGGGGAAAACCTTATTTATCAGCCGGAAAACCTACCGGATTGATGGTAGTGGTCAAATGGCGATTACCGTTGATGTTGAAGTGGCGAGCGATACACCGCATCCGGCGCGGATTGGCCTGAACTGCCAGCTGGCGCAGGTAGCAGAGCGGGTAAACTGGCTCGGATTAGGGCCGCAAGAAAACTATCCCGACCGCCTTACTGCCGCCTGTTTTGACCGCTGGGATCTGCCATTGTCAGACATGTATACCCCGTACGTCTTCCCGAGCGAAAACGGTCTGCGCTGCGGGACGCGCGAATTGAATTATGGCCCACACCAGTGGCGCGGCGACTTCCAGTTCAACATCAGCCGCTACAGTCAACAGCAACTGATGGAAACCAGCCATCGCCATCTGCTGCACGCGGAAGAAGGCACATGGCTGAATATCGACGGTTTCCATATGGGGATTGGTGGCGACGACTCCTGGAGCCCGTCAGTATCGGCGGAGTTCCAGCTGAGCGCCGGTCGCTACCATTACCAGTTGGTCTGGTGTCAAAAATAA//.

The basic idea was to exchange part of the mCMV promoter (mCMV-P)element sequence with the human CMV promoter (hCMV-P) element thatincludes the TetO binding sites responsible for regulation bytetracycline (Tet). This construct, JV57_JV56_pJV39_pJV10 (hereinabbreviated as “pJV57”; FIG. 7), includes the tetracycline-sensitiveTetO regulatory element for expression of LacZ. FIG. 10 showsschematically the hCMV-P/TetO inserted into the mCMV promoter sequence.This insertion replaces part of the mCMV-P promoter sequence with a partof the hCMV-P promoter sequence. Another construct was made toincorporate expression-increasing changes in a hCMV promoter describedby Patwardhan et al. in the context of an unregulated promoter (hybridmCMV enhancer/(partial) hCMV promoter/rat EF-1alpha intron). (Patwardhanet al., “High-resolution analysis of DNA regulatory elements bysynthetic saturation mutagenesis”, Nature Biotechnology 27(12):1173-75(2009)). This construct was JV59_JV56_pJV39_pJV10 (abbreviated herein as“pJV59”; FIG. 8). In another construct, JV60_JV56_pJV39_pJV10 (hereinabbreviated as “pJV60”; FIG. 9), the TetO sequences of pJV57 werechanged to match the sequences that increased expression surrounding thetranscription start site in the study by Patwardhan et al. (see, FIG. 9and FIG. 12).

FIG. 11 shows the DNA sequence of hCMV-P/TetO that we used to replacethe mCMV promoter (mCMV-P) sequences. Arrows indicate palindromic TetRbinding sites. The mCMV-P and hCMV-P promoter sequences shown are thosesequences from the TATA box through the start site of transcription. Thetranscription start is the g residue in the 3′ sequence taccg. Note thatthe TetO sequence most certainly impacts the transcription start site,since the transcription start site is typically ˜30 bases 3′ to the 5′ Tof the TATA box.

We expressed beta-galactosidase from various constructs to monitor thelevel of protein expression. This inserted substitute sequence, whichincludes muCMV enhancer element (mCMV-E)/(partial) huCMVpromoter/TetO/ratEF-1alpha intron, was indeed regulated by tetracyclinein the medium (See, e.g., FIG. 14, pJV57+/−Tet). Furthermore, theconstruct pJV57 yielded approximately 10-fold as much recombinantprotein as a human CMV/TetO control (pcDNA5/TO/LacZ; Thermo FisherScientific), when Tet was present in the medium, but about 3.5-fold lessbeta-galactosidase in the absence of tetracycline, as shown in FIG. 14.T-Rex CHO cells bearing the muCMV enhancer/ratEF-1alpha intron hybridpromoter in pJV56, absent a TetO sequence within the CMV-P segment ofthe mCMV enhancer sequence, also expressed approximately 10 times moreprotein than the human CMV/TetO control (pcDNA5/TO/LacZ), regardless ofwhether tetracycline was in the medium.

Materials and Methods

T-REx™-CHO cells. T-REx-CHO cell line (Thermo Fisher Scientific, ProductNo. R71807) were cultured in Ham's F12 medium+glutamine+10 μg/ml Blastper manufacturer's protocol. T-REx-CHO cells were electroporated usingthe long duration electroporation (LDE) method as described by Bodwellet al. (Bodwell et al., “Long Duration Electroporation for AchievingHigh Level Expression of Glucocorticoid Receptors in Mammalian CellLines”, J. Steroid Biochem. Molec. Biol. 68:77-82 (1999)), with variousconstructs pJV56, pJV57, pJV59, and pJV60, expressing thebeta-galactosidase protein, as shown in FIG. 6, FIG. 7, FIG. 8, and FIG.9, respectively. Transfected cells were allowed to recover for 24 hoursand then were treated with or without 1 μg/ml tetracycline for 24 hours.Cells were lysed and beta-galactosidase activity was assayed using aβ-Gal Assay Kit per manufacturer's protocol (Thermo Fisher Scientific,Product No. K1455-01). Briefly, lysates were diluted 10-fold and 10-μlaliquots were assayed using a BCA protein assay kit (Thermo FisherScientific, Product No. 23227) to determine protein concentration of thelysate. Lysates were diluted 100-fold and 10-μl aliquots were assayedfor beta-galactosidase activity. All samples were transfected at leastin duplicates. Specific beta-galactosidase activity was normalized tothe amount of protein assayed and background activity ofmock-transfected cells was subtracted from transfected samples. Resultswere graphed with standard deviation shown (FIG. 14).

CHO-K1/TetR cells. In separate experiments, tetracycline repressor(TetR) was subcloned by Genscript® (Piscataway, N.J.) intopcDNA3.1+expression vector to yield vector pJV40_pcDNA3.1+tetR(abbreviated herein, as “pJV40”; FIG. 15). CHO-K1 cells were routinelycultured in PowerCHO™ 2 Chemically Defined, Serum-free CHO Medium(Lonza, Product No. BE12-771Q), and cells were electroporated using theLDE method, as described above for pJV40. Transfected pools wereselected for 10 days in PowerCHO™ 2+600 μg/ml G418 (Gibco, Product No.10131027). Cells were then serially diluted and plated in 96-wellmicroplates (Corning® CellBIND® 96 Well, Product #3340) at 0.75 cell perwell in cloning medium (EX-CELL® 302 Serum-Free Medium for CHO Cells;Sigma-Aldrich, Product No. 14326C SIGMA)+15% conditioned medium in thepresence of G418). Clonal populations were identified after 11-12 daysand were transferred to 12-well plates in 50/50 cloning medium/PowerCHO™2 medium for an additional 3-4 days. Finally, clones were moved andgrown in a 24 deep-well plate (VWR, Product No. P-DW-10ML-24-C-S) withconstant shaking (220 rpm) in PowerCHO™ 2 medium+600 μg/ml G418.

To screen for clones expressing high levels of TetR, CHO-K1/TetR cloneswere transfected with pJV57 using the ExpiFectamine™ CHO transfectionkit (Thermo Fisher Scientific, Product No. A29130) per manufacturer'sprotocol. From those highly expressing TetR clones, some clones weresubsequently chosen to be transfected with vector pJV56, pJV57, pJV59,or pJV60, using the ExpiFectamine™ CHO transfection kit (Thermo FisherScientific, Product No. A29130), again transfected per manufacturer'sprotocol. Transfected clones were allowed to recover for 24 hours andthen were treated with 1 μg/ml tetracycline for 24 hours. To measureexpression of the LacZ protein product, cells were lysed, andbeta-galactosidase activity was assayed using a β-Gal Assay Kit permanufacturer's protocol (Thermo Fisher Scientific, Product No.K1455-01).

Briefly, lysates were diluted 10-fold and 10-μl aliquots were assayedusing a BCA protein assay kit (Thermo Fisher Scientific, Product No.23227) to determine protein concentration of the lysate. Ten (10) μl ofundiluted lysate was assayed for beta-galactosidase activity. Allsamples were transfected at least in duplicates. Specificbeta-galactosidase activity was normalized to the amount of proteinassayed and background activity of mock-transfected cells was subtractedfrom transfected samples. Results were graphed with standard deviationshown (e.g., FIG. 16, FIG. 17, FIG. 18).

FIG. 16 (clone 3E7), FIG. 17 (clone 3F9), and FIG. 18 (clone 4G2) showsrepresentative results from CHO-K1/TetR clones transfected with variousconstructs (pJV56, pJV57, pJV59, and pJV60) expressing thebeta-galactosidase protein (or transfected with positive control:pcDNA5/TO/LacZ; Thermo Fisher Scientific, Product No. V1033-20). Asabove, cells were transfected with pJV57 using the ExpiFectamine™ CHOtransfection kit (Thermo Fisher Scientific, Product No. A29130) permanufacturer's protocol. Transfected clones were allowed to recover for24 hours and then were treated with 1 μg/ml tetracycline for 24 hours.Cells were lysed, and beta-galactosidase activity was assayed using aβ-Gal Assay Kit per manufacturer's protocol (Thermo Fisher Scientific,Product No. K1455-01). Briefly, lysates were diluted 10-fold and 10-μlaliquots were assayed using a BCA protein assay kit (Thermo FisherScientific, Product No. 23227) to determine protein concentration of thelysate. Ten (10) μl of undiluted lysate was assayed forbeta-galactosidase activity. All samples were transfected at least induplicates. Specific beta-galactosidase activity was normalized to theamount of protein assayed and background activity of mock-transfectedcells was subtracted from transfected samples. Specificbeta-galactosidase activity was normalized to the amount of proteinassayed and background activity of mock-transfected cells was subtractedfrom transfected samples. Results were graphed with standard deviationshown.

Results

T-REx™ CHO cells. In experiments using T-RExCHO cells (Thermo FisherScientific), a commercial cell line that stably expresses TetR, wemeasured beta-galactosidase (beta-gal) activity as a readout to test theability of pJV57 to be regulated by tetracycline (Tet). As shown in FIG.14, pJV57 had equivalent expression to pJV56 when induced by thepresence of tetracycline (+Tet). In addition, pJV57 had approximately10-fold higher expression of LacZ in the presence of tetracycline (+Tet)when compared with pcDNA5/TO/LacZ, a vector shown to exhibit robusttetracycline-regulated expression. pJV57 also showed 3.5-fold regulatedexpression by tetracycline, a key observation demonstrating a powerfullyregulated promoter. Fold-difference in Tet regulation for the positivecontrol pcDNA5/TO/LacZ was not included in FIG. 14, because of lowsignal-to-noise ratio between uninduced pcDNA5/TO/LacZ and background,resulting in a negative specific beta-gal activity in the control.

In an attempt to further improve upon pJV57, we hypothesized that theTetO sequences could reduce expression from pJV57 as previous studiesshowed that changes around the transcription start site reducedexpression from the hCMV promoter (Patwardhan et al., “High-resolutionanalysis of DNA regulatory elements by synthetic saturationmutagenesis”, Nat Biotechnol. 27(12): 1173-1175 (2009)). The TetOsequences in pJV57 were changed to match the sequences that increasedexpression surrounding the transcription start site in the study byPatwardhan et al. (pJV60, FIG. 9 and FIG. 12). Furthermore, thesechanges were designed to maintain high affinity TetR binding (theaffinity of different TetO mutations is described in Sizemore et al. andreviewed in Hillen and Berens). (See, Sizemore et al., “Quantitativeanalysis of Tn10 Tet repressor binding to a complete set of tet operatormutants”, Nucleic Acids Research 18 (10) 2875-2880 (1990); Hillen andBerens, “Mechanisms underlying expression of Tn10 encoded tetracyclineresistance”, Ann. Rev. Micro. 48:345-369 (1994)). However, thisoptimized construct, pJV60, did not appear to increase expressioncompared to pJV57 in T-REx-CHO cells (FIG. 14). Tetracycline-regulatedexpression was maintained, but potentially slightly less regulation(2.68-fold compared to 3.50-fold (FIG. 14).

The optimized hCMV promoter (hCMV-P) sequences replaced the mCMVpromoter (mCMV-P) sequences in the mCMV enhancer sequence/rat EF-1aintron hybrid promoter of the invention (see, sequence comparison inFIG. 13). The changes incorporated into pJV59 did not appear to increaseexpression relative to pJV56 (FIG. 14). Thus, we conclude that in theT-REx-CHO cells, the context of the powerful mCMV enhancer/promoter-ratEF-1a intron, that changes around the transcription start site havelittle or no impact on expression.

CHO-K1/TetR cells. In separate experiments, a CHO-K1 cell line stablyexpressing TetR was generated by transfection of pJV40 (see, FIG. 15)that has TetR gene subcloned into pcDNA3.1+ vector. Geneticin-resistantCHO-K1 pools were serially diluted to obtain single-cell colonies andscreened to have high expression of TetR, i.e. more than two-foldrepression of LacZ in the absence of Tet (data not shown). Three cloneswere selected for further analysis, as shown respectively in FIG. 16,FIG. 17, and FIG. 18, referred to herein as CHO-K1/TetR clones. Theclones were transiently transfected with pcDNA5/TO/LacZ as a control,and expression vectors of the present invention, i.e., vectors pJV56,pJV57, pJV59 and pJV60, as described above, to determine theeffectiveness of a Tet-regulated promoter element based on the mCMVenhancer sequence/rat EF-1a intron hybrid promoter sequences usingTetR-expressing cells that were generated in-house.

As shown in FIG. 16, FIG. 17, and FIG. 18, pJV56 in two of the 3CHO-K1/TetR clones exhibited 2- to 3-fold higher expression of LacZcompared to pcDNA5/TO/LacZ in the presence of tetracycline (+Tet).Addition of hCMV-P/TetO sequences in pJV57 enabled protein expression tobe regulated by tetracycline to the extent of 3.24-, 9.30- and 3.15-foldenhancement of LacZ expression in the presence of tetracycline (+Tet),compared to (−Tet) (see, pJV57, in FIG. 16, FIG. 17, and FIG. 18respectively), although the level of expression was variable dependingon the clone studied. This is comparison to pJV56, which did not includethe hCMV-P/TetO sequences (1.27-, 0.95-, 1.19-fold differences between+Tet and minus-Tet treatments, as shown in FIG. 16, FIG. 17, and FIG.18, respectively).

Interestingly, total expression of LacZ was increased in all threepJV59-transfected CHO-K1/TetR clones, although as expected there wasessentially no tetracycline-sensitive regulation of expression (±Tetcomparison: 0.99-, 1.06-, 1.00-fold difference), as shown in FIG. 16,FIG. 17, and FIG. 18, consistent with our hypothesis that proteinexpression can be increased by optimizing sequences surrounding thetranscription start site (see, Patwardhan et al.). However, addition ofTetO sites that were mutated to maintain TetR binding (pJV60)—in thecontext of the optimized promoter—showed decreased (FIG. 16, FIG. 17) orunchanged (FIG. 18) LacZ expression compared to pJV59. Nevertheless,LacZ expression was augmented in all three pJV60-bearing clones comparedto pJV57, in the presence of tetracyclin (2.31-, 2.82- and 1.56-foldhigher expression compared to its non-Tet-treated control; FIG. 16, FIG.17, FIG. 18, respectively). This suggests that mutation of TetOsequences adversely affected TetR binding as observed by higher basalLacZ expression in all clones in the absence of Tet and lowerfold-induction upon +Tet addition.

Overall, all of the pJV56, pJV57, pJV59, and pJV60 constructs inCHO/TetR cells demonstrated increased LacZ expression compared to CHOcells expressing from pcDNA5/TO/LacZ (i.e., positive controls) in thepresence of tetracycline, and CHO cells bearing the inventive hybridpromoter with hCMV-P/TetO sequences had beta-galactosidase expressionup-reregulated by tetracycline (1.56- to 9.30-fold differences),compared to (−Tet), as shown in FIG. 16, FIG. 17, and FIG. 18. It shouldbe noted that the method of transfection is different between T-REx-CHOcells (adherent) to CHO-K1/TetR cells (cell suspension in liquid aqueousmedium), and that transfection efficiency may account for differencesobserved in the overall levels of specific beta-galactosidase activity.

Example 4. Limiting the Metabolic Burden of Recombinant ProteinExpression During Selection Yields Pools with Higher Expression Levels

We sought to test the idea that the metabolic burden of any recombinantprotein expression, if high enough, would impact the selection processduring CHO cell line development. We first developed an inducibleexpression system by isolating tetracycline repressor (TetR) expressingCHO cell lines (see, Example 3 hereinabove), and then transfected theseTetR cell lines with expression vectors expressing either a Fc fusionprotein or a recombinant antibody. Neither of the proteins displayedobvious toxicity in constitutive expression systems. For these twoproteins, we show that pools that were induced to express a recombinantprotein expression during cell line selection had lower titers thanpools that were uninduced during cell line selection. These data areconsistent with the hypothesis that the metabolic burden of proteinexpression selects against the higher expressing clones during selectionof cell pools.

Materials and Methods

Cell Culture. CHOK1 GS KO cells (Horizon Discovery) were maintained inCD OptiCHO™ (Gibco)+4 mM glutamine (Q). Cells were passaged every 3-4days at a seed density of 0.3-0.4×10⁶/mL. A codon optimized tetracyclinerepressor (TetR) was synthesized (Genscript) and subcloned into anexpression vector with human CMV driving TetR expression. GS KO cellswere electroporated using the LDE method as described (Bodwell et al.,Long Duration electroporation for achieving high level expression ofglucocorticoi receptors n mammalian cell lines, J. Steroid Biochem. Mol.Biol. 68(8):77-82 (1999)) with TetR vector. Transfected pools wereselected for about 12 days in CD OptiCHO™+glutamine +400 μg/ml G418(Gibco). Pools were then transfected (as described below in thetransient transfection section) with pcDNA5/TO/LacZ (ThermoFisher),allowed to recover for 24 hours and then treated with or withouttetratcycline (Tet, 1 μg/mL) for 24 hours to identify the pool with highTet-dependent induction of the target gene. Cells were lysed, andbeta-galactosidase activity was assayed using a β-Gal Assay Kit permanufacturer's protocol (ThermoFisher Scientific) and read on SpectraMax 5 plate reader (Molecular Devices). Briefly, lysates were diluted10-fold and 10 μl was assayed using a BCA protein assay kit(ThermoFisher) to determine protein concentration of the lysate. Tenmicroliters (10 μL) of undiluted lysate was assayed forbeta-galactosidase activity. Tet and a more stable derivative,doxycycline (Dox), were used to induce cultures, as described herein.

The selected pool was then serially diluted and plated in 96-wellmicroplates (Corning® CellBIND®) at 0.75 cells per well in cloningmedium (EX-CELL® 302 Serum-Free Medium for CHO Cells)+15% conditionedmedium in the presence of G418). Clonal populations were identifiedafter 11-12 days (CloneSelect Imager, Molecular Devices) and transferredto 12-well plates in 50/50 cloning medium/CD OptiCHO™ medium for anadditional 3-4 days. Finally, clones were transferred to 24 deep-wellplates (VWR) with constant shaking (220 rpm) in CD OptiCHO™medium+glutamine+400 μg/ml G418.

To screen for clones expressing high levels of TetR, clones weretransfected with pcDNA5/TO/LacZ or an in-house plasmid expressing LacZusing the HCN protocol (see, Transient transfection section, below).Transfected clones recovered for 24-48 hours and then were treated with1 μg/mL Tet for 24 hours. Cells were lysed, and beta-galactosidaseactivity was assayed using a β-Gal Assay Kit per manufacturer's protocolas described above. All samples were transfected at least in duplicate.Specific beta-galactosidase activity was normalized to the amount ofprotein assayed and background activity of mock-transfected cells wassubtracted from transfected samples.

Transient transfection. Cells were passaged to 1×10⁶/mL the day beforetransfection. On the day of transfection, cells were counted on aVi-Cell XR (Beckman Coulter) and electroporated using the high copynumber (HCN) protocol (see, Barsoum J., Introduction of stablehigh-copy-number DNA into Chinese hamster ovary cells byelectroporation, DNA Cell Biol. 9(4):293-300 (1990)) in duplicate ortriplicates. Briefly, 1×10⁶ cells were used per transfection. Cells werespun down and resuspended in 150 μl of PF CHO medium (Sigma Aldrich) andaliquoted into one well of a 5×5 electroporation plate (BTX). Tenmicrograms (10 μg) of plasmid DNA and 10 μg of salmon sperm DNA (SigmaAldrich) were used per transfection. PF CHO medium was used to bringfinal transfection volume up to 50 μL, and aliquots were placed intoappropriate wells in the 5×5 electroporation plate. For mock-transfectedsamples, salmon sperm DNA was used only. Cells were electroporated underthese conditions: 290V voltage, 950 μF capacitance, 950 ohm resistancein an ECM 630 electro manipulator coupled to a HT-100 high throughputadaptor (BTX). After electroporation, cells were transferred to a 24deep well plate containing 1 mL of fresh growth medium withoutantibiotics and were allowed to recover for 2 days. Two dayspost-transfection, a duplicate 24 deep well plate was generated fromhalf of the cells in each well and treated with 1 μg/mL tetracycline(Tet; Sigma Aldrich). On days 4, 6 and 8, cells were fed with 10% CDEfficient Feeds (Thermo Fisher Scientific) A+B+C (3.3% each) and 1 μg/mLTet.

Stable transfection. Cells were passaged to 1×10⁶/mL the day beforetransfection and counted on a Vi-Cell the day of transfection, asdescribed above. Cells were electroporated using the long-durationmethod (Bodwell et al., Long Duration electroporation for achieving highlevel expression of glucocorticoi receptors n mammalian cell lines, J.Steroid Biochem. Mol. Biol. 68(8):77-82 (1999)) in, at least, duplicatecultures. For each transfection 20×10⁶ cells were used. Cells were spundown, resuspended in 300 μL PF CHO medium (Sigma) and aliquoted into a4-mm electroporation cuvette (VWR International). Meanwhile, a DNA/RNAmixture was prepared. For each transfection, a total of 25 μg DNA/RNAwas mixed with PF CHO to a final volume of 50 μL. For the transposonexperiments, 22.5 μg of transposon and 2.5 μg of transposase RNA (10%)was used. For mock-transfected cells, DNA/RNA were omitted from the PFCHO mixture. Cells were electroporated under these conditions: 200Vvoltage, 725 μF capacitance, 3175 ohm resistance in an ECM 630 electromanipulator coupled to a 630B safety stand (BTX; See, Barsoum J.,Introduction of stable high-copy-number DNA into Chinese hamster ovarycells by electroporation, DNA Cell Biol. 9(4):293-300 (1990)). Afterelectroporation, cells were resuspended in 15 mL of fresh growth medium,+glutamine, without antibiotics and allowed to recover for 2 days in astationary T75 flask. After this recovery period, cells were counted ona Vi-Cell and were seeded for selection at 0.75 to 1×10⁶/mL in CDOptiCHO™ medium (Gibco), −Q+antibiotics (as needed) in a 24 deep wellplate shaking at 220 rpm. Cells were counted and passaged every 3-4 dayson a Guava® easyCyte™ flow cytometer (MilliporeSigma). In some cases,cells were treated with doxycycline (Dox; Sigma D9891) to a finalconcentration of 0.5 μg/mL. In all cases, there was a replicate cultureplate without Dox as a control for +Dox cultures.

Fed batch production. Cells were seeded by dilution into a CD OptiCHO™or CD FortiCHO™ (Gibco) production medium to a density of0.7-1.5×10⁶/mL. On day 0, production medium was frontloaded with 30% CDEfficient Feeds A, B and C (10% of each feed). On days 3, 6 and 8 ofproduction, cells were fed with 10% CD Efficient Feeds A, B and C (3.3%of each feed) and glucose was added as necessary to a finalconcentration of about 10 g/L. Growth profiles (viable cell density andviability) were also measured on days 3, 6 and 8 on a Guava® easyCyte™flow cytometer (MilliporeSigma). Glucose was measured using acolorimetric assay (Stanbio Laboratory) on a Spectra Max 5 plate reader(Molecular Devices). The measurement of titer measurements was performedby affinity High Performance Liquid Chromatography (HPLC) using POROSA/20 Protein A column. For the interval between days [m, n], Specificproductivity (qP) was calculated according to the formula:qP=titer_(n)/∫_(m) ^(n) VCDdt/(t_(n)−t_(m)), where and time (t) isexpressed in days.

Quantitative PCR (qPCR). On day 3 of production, anywhere from 200,000to 2×10⁶ cells were isolated, spun down and resuspended vigorously in300 μL RA 1 buffer (Macherey-Nagel)+1% B-ME (Sigma). Cell lysates werefrozen at −70° C. until ready for automated purification on a BioRobot(Qiagen) using a NucleoSpin RNA kit (Macherey-Nagel). The concentrationof RNA was measured on a Nanodrop spectrophotometer (Thermo Fisher)before qPCR set up. Once concentrations were determined on the Nanodrop,RNA was diluted to 5-10 ng/μL. Two microliters (2 μL) was used as atemplate in a 20-μL reaction. qScript XLT 1-step RT-PCR kit (Quanta) orthe Luna Universal 1-step RT-qPCR kit (New England Biolabs) was usedaccording to manufacturer's protocol. Transcripts of interest werenormalized to GAPDH and beta-actin. Ratios of LC/HC were calculated bydividing the relative fold-change of LC by the relative fold-change ofHC. The primer sequences used are listed below in Table 1, in a 5′ to 3′orientation.

TABLE 1 Primer sequences employed. GAPDH CCTGGAGAAACCTG ForwardCCAAGTATGA// SEQ ID NO: 36 GAPDH AGAAGGTGGTGAAG Probe: 5′ CAGGCATCTGAGGGCy5- CC// labeled SEQ ID NO: 37 GAPDH ACTGTTGAAGTCGC Reverse AGGAGACAA//SEQ ID NO:38 Beta- CCCAGCACCATGAA actin GATCAA// Forward SEQ ID NO: 39Beta- CATTGCTCCTCCTG actin AGCGCAAGTA// Probe: 5′ SEQ ID NO: 40Fluorescein (6-FAM)- labeled Beta- TGCTTGCTGATCC actin ACATCTC// ReverseSEQ ID NO: 41 Glutamine GGGAACAGATGGG synthetase CACCCTTT// (GS)SEQ ID NO: 42 Forward GS Probe: TTGGCCTTCCAAT 5′ GGCTTTCCTGGGC//Hexachloro- SEQ ID NO: 43 Fluorescein (Hex)- labeled GS ReverseACGATATCCCTGCC ATAGGCTTTGT// SEQ ID NO: 44

Results

Generation of a TetR-expressing CHO-K1 (GS KO) clone. A CHO-K1 glutaminesynthetase (GS) knock out (GS KO, Horizon Discovery) cell line stablyexpressing TetR was generated by transfection of a plasmid that has theTetR gene subcloned into a vector with human CMV driving expression ofTetR. (Yao, F. et al., Tetracycline Repressor, tetR, rather than theCell Transcription Factor Fusion Derivatives, Regulates Inducible GeneExpression in Mammalian Cells, Hum Gene Ther. 9:1939-1950 (1998)).Geneticin-resistant CHO-K1 (GS KO) pools (TetR-GS KO) were seriallydiluted to obtain single-cell colonies and screened to have highexpression of TetR. This was achieved by transient transfection ofTetR-GS KO clones with pcDNA5/TO/LacZ, a vector expressing the reporterenzyme beta-galactosidase under the control of a Tet-regulatable hCMVpromoter. The top clones were selected based on their ability to repressexpression of LacZ by more than two-fold (data not shown).

Regulation of an Fc-fusion protein expression in a TetR-GS KO clone. Arepresentative TetR-GS KO clone, 9G1, was selected for further analysis(FIG. 25A-B). Clone 9G1 was transiently transfected with a vector systemexpressing a recombinant Fc-fusion protein (Fc-A) under the control of aTet-regulated hybrid promoter, pJVec_1, as described in Examples 1-3,herein (FIG. 25A, each point on the graph represents a transfectionreplicate). A constitutive hybrid promoter identical to the induciblepromoter except lacking TetO sequences was used as a control (FIG. 25A).Two days post-transfection, transfectants were treated with 1 μg/mltetracycline (Tet) to induce Fc-A expression while a duplicate plate wasleft untreated as a control. FIG. 25B shows that upon treatment withTet, there is a 2-fold and 2.4-fold increase in Fc-fusion titer and qP,respectively, in pJVec_1 transfected cells. As expected, we saw thatcells transfected with the control vector were not responsive to Tet andconstitutively expressed recombinant Fc-A protein.

Description of inducible transposon-based system. Next, we sought todetermine the relationship between recombinant protein production andcellular growth. We expressed an Fc-fusion protein, Fc-A, by using aninducible transposon-based vector system. As described in FIG. 25A-B,Fc-A expression was driven by the promoter consisting of mCMV/TPL/ratEF-1a intron and glutamine synthetase was used as the selectable marker.Transposon vectors were co-transfected with a transposase in a 4:1(donor transposon:transposase) mass ratio to promote transposition oftarget genes. 9G1 cells require glutamine supplementation in the mediumfor survival and thus, cells that have stably integrated the targetprotein (Fc-A) and GS can be selected in medium lacking glutamine. Toincrease stringency of selection and isolate high-producing cells, 75 or100 μM L-methionine sulfoximine (MSX) was added to the medium duringstable pool generation. (Fan, L. et al., Improving the efficiency of CHOcell line generation using glutamine synthetase gene knockout cells,Biotechnol Bioeng. 2012; 109(4):1007-1015 (2012); Rajendra, Y. et al.,Generation of stable Chinese hamster ovary pools yielding antibodytiters of up to 7.6 g/L using the piggyBac transposon system, BiotechnolProg. 32(5):1301-1307 (2016)). Additionally, transfectants were treatedwith 0.5 μg/mL doxycycline (Dox) to induce Fc-A expression or withoutDox, as a control, during the selection process.

The relationship between growth and CHO-K1 cell productivity levels. Totest the inducible transposon-system, 9G1 cells were stably transfectedwith pJVec_2 or pJVec_3, constitutive or Dox-regulatable, respectively,transposon vectors expressing Fc-A protein (FIG. 19A). As expected, Doxtreatment did not alter the growth profiles of cells transfected withthe constitutive pJVec_2 plasmid (FIG. 19B). Induction of recombinantFc-A expression upon Dox treatment significantly decreased VCD andviability of pJVec_3-transfected cells during selection (FIG. 19B). FIG.1B shows that pJVec_3-transfected cells recovered to >90% viability in13 days when expression of Fc-A production was repressed in mediumlacking Dox. In contrast, pJVec_3 cells selected in the presence of Doxrequired 16 days to achieve >90% viability. The cells selected at 100 μMMSX also recovered in 13 days when Fc-A protein expression was repressed(data not shown) and more than 23 days when selected in the presence of100 μM MSX (FIG. 26). Interestingly, the growth profiles of inducedpJVec_3 cells in the presence of Dox (FIG. 26) at both 75 and 100 μM MSXalmost overlap with the growth profile of cells expressing Fc-Aconstitutively (pJVec_2, FIG. 26), implying that the observed decreasein VCD and viability upon Dox addition in pJVec_3-expressing cells weredue to the metabolic burden of producing Fc-A, further supporting thehypothesis that “unnecessary” protein production can hinder robustcellular growth.

Cell pools derived as described above were put into a small-scale 10-dayfed-batch process once recovered from selection. Cell lysates andsupernatants were harvested on days 3 and 10 for mRNA analysis and Fc-Atiter quantification, respectively. FIG. 20A shows growth and viabilityprofiles of pJVec_2 and pJVec_3 transfected pools, and FIG. 20B showsday 10 Fc-A titers and specific productivity of pJVec_2 cells (lanes1-2: 75 μM MSX; lanes 6-7: 100 μM MSX) and pJVec_3 cells (lanes 3-5: 75μM MSX; lanes 8-10: 100 μM MSX). Lanes 1, 4, 6, and 9 did not receiveDox treatment while lanes 2, 3, 7, and 8 received Dox throughoutselection and production, as indicated. Lanes 5 and 10 received Dox onlyin production. There is a 16-20 fold increase in Fc-A titer and an 8-10fold increase in qP upon Dox addition in pJVec_3 cells (lanes 4-5 and9-10, FIG. 20A-C). The pJVec_3(−) production cultures without Doxgenerally achieved lower cell densities and had lower viabilities whencompared to pJVec_3(−) cultures treated with Dox for reasons that arenot clear (FIG. 20A). This effect was observed in both the 75 μM MSX and100 μM MSX treated cells. Control pJVec_2 cells were unresponsive to Doxand had titers and qP in the range of pJVec_3 cells that received Doxtreatment during selection (compare lanes 1 and 2 to lane 3 and lanes 6and 7 to lane 8, FIG. 20B). Production titers and qP in pools weresimilar when pools were selected at 75 μM MSX or 100 μM MSX, despite thegreater impact of 100 μM MSX on VCD and viability during selection.

Next, we evaluated whether pools selected without the pressure ofproducing a recombinant product (culture medium lacking Dox) would haveincreased proportions of inherently high-producing cells within thepopulation due to their ability to grow as well as low producers, whichdo not have the metabolic burden of producing as much recombinantprotein as high producers. To this end, pJVec_3(−) cells that had Fc-Aexpression turned off during selection were induced with Dox duringproduction (lanes 5 and 10, FIG. 20B). Cells selected in 75 μM MSX had amedian titer and qP of 1.005 g/L and 33 pg/cell/day, respectively, whichis about a 5-fold increase in Fc-A titer and about a 4-fold increase inqP compared to cells that had Dox present in the medium throughoutselection (compare lanes 3 and 5). Likewise, cells selected in 100 μMMSX had a about a 5-fold and about a 3.6-fold increase in Fc-A titer andqP, respectively, compared to cells selected with Dox present (comparelanes 8 and 10). These data support the hypothesis that pools withhigher productivities can be isolated when cells are maintained in astate that does not require excess production of a recombinant protein,likely due to their ability to grow as well as pools with lowproductivity.

Relationship of Fc-fusion recombinant message levels to CHO cellproductivity. Previous reports have shown qP to have a strong positivelinear relationship with recombinant protein transcript levels in thecell. (See, Fomina-Yadlin, D. et al., Transcriptome analysis of a CHOcell line expressing a recombinant therapeutic protein treated withinducers of protein expression, J. Biotechnol. 212:106-115 (2015); Lee,C. J. et al., A clone screening method using mRNA levels to determinespecific productivity and product quality for monoclonal antibodies,Biotechnol. Bioeng. 2009. doi:10.1002/bit.22126). In order to determinewhether mRNA levels correlated to qP under different selectionconditions, RNA was purified from cells on day 3 of production from theexperiment shown in FIG. 20A and Fc-A transcript levels were analyzed byquantitative RT-PCR (qPCR). All samples were normalized relative to oneof the regulatable pJVec_3(−) expressing pools with Fc-A expressionturned off (−Dox). Consistent with published reports, we saw a positivelinear relationship between qP and relative Fc-A transcript levels (FIG.20C). Importantly, pools of pJVec_3(−) that were induced with Dox onlyduring production managed to increase Fc-A transcript levels by ˜5-6fold, resulting in qP values ranging from 33-59 pg/cell/day (X symbols,highlighted in dashed oval), whereas pJVec_3 pools that wereconstitutively induced (+ symbols) and pools transfected withconstitutive plasmid pJVec_2 (* symbol) reached a maximum of −2-foldincrease in Fc-A transcript levels (FIG. 20C).

Regulatable expression of a monoclonal antibody (mAb). We then testedwhether this regulated expression system would have any advantages whenused to express mAbs. The schematic representation of the plasmid asdepicted in FIG. 21A shows light chain (LC) and heavy chain (HC) ofmAb_A driven by a murine CMV promoter linked to a rat EF-1α intron asdescribed herein above. This vector also encodes the GS selectablemarker. 9G1 cells were electroporated with pJVec_4 and a mRNA encoding atransposase. Stable transfectants were selected in medium lackingglutamine and Dox. We observed a robust recovery of all pools whilemock-transfected cells declined rapidly in viability and never recovered(data not shown). As before, pools were subjected to Dox treatment in a10-day fed-batch production to determine the level of mAb_A expression(FIG. 21B). A replicate plate was cultured in the absence of Dox as acontrol. There is a ˜3.4-fold increase in mAb_A titer and qP upon Doxinduction, verifying the function of our pJVec_4 expression vector (FIG.21B).

Differential mAb LC and HC transcript levels during production. To gaina deeper understanding of mAb production with the pJVec_4 expressionvector, levels of LC and HC mRNA expression was analyzed by qPCR. Onereplicate of the pJVec_4 pools that did not receive Dox was used as acontrol sample. When we looked at relative expression of LC or HC mRNAas a function of qP, we saw two distinct populations, separated by mAb_Aexpression being turned on or off, i.e. +Dox or −Dox, respectively (FIG.21C), suggesting that increased LC or HC expression led to higher qPvalues. While the expression of both LC and HC transcripts increase, thelevel by which LC increases is more than that of HC (FIG. 21C, note thedifference in scale). To show this another way, the ratio of LC to HCwas calculated and we show that, on average, the increase in ratio of LCto HC is ˜4.5 times comparing −Dox and +Dox (FIG. 21D). We hypothesizedthat the polyA sequence in pJVec_4 downstream of LC was not sufficientfor transcription termination and thus, the transcriptional unit of LCwas interfering with that of HC (Eszterhas, S. K. et al.,Transcriptional interference by independently regulated genes occurs inany relative arrangement of the genes and is influenced by chromosomalintegration position, Mol. Cell Biol. 22(2):469-479 (2002)), resultingin the observed imbalance of LC and HC mRNA levels and high LC/HC ratiospost-induction.

To test this hypothesis, the polyA sequence downstream of LC in pJVec_4was replaced with a human β-globin polyA/terminator sequence. (Dye, M Jand Proudfoot, N J, Multiple transcript cleavage precedes polymeraserelease in termination by RNA polymerase II, Cell 105(5):669-681(2001)). This construct, pJVec_5 (FIG. 22A) along with transposase mRNA,was used to transfect Clone 9G1 and three other GS KO clonal cell linesstably expressing the TetR protein (FIG. 22B). The parental GS KO hostsnot expressing TetR were included as a control and as expected, whenselected in medium lacking glutamine, Dox treatment did not alter therecovery profile of these pools. In contrast, in all four TetR-GS KOclonal cell lines that were transfected with pJVec_5, we observeddecreased cell growth when pools were selected in the presence of Doxcompared to its −Dox control, consistent to what was described in FIG.1B (FIG. 22B). Several pJVec_5 pools selected in the absence of Dox werethen placed in +Dox conditions, and the doubling time was measured for a4-day culture. The doubling time during passage increased from 18.6hours to 21.3 hours (n=2) upon Dox treatment indicating the additionalprotein expression burden decreased cell growth even after going throughthe selection process.

Improved productivity in pJVec_5 pools selected and maintained in theabsence of doxycycline (Dox). Pools of pJVec_5-transfected cells werethen subjected to a 10-day fed-batch production assay. Pools that wereselected in the presence of Dox were maintained in that fashionthroughout the production assay (FIG. 5A, lanes 1, 3, 5, 7).Additionally, pools that were selected in the absence of Dox weretreated with Dox during production to induce mAb_A expression (FIG. 23A,lanes 2, 4, 6, 8). These pools had increased qP and titers compared topools that had mAb_A expressed constitutively; there was about a 1.3- to2-fold increase in mAb_A titer and about a 1.2-fold increase in qP,depending on which clonal cell line studied (FIG. 23A). The GS KO hostnot expressing TetR had similar or lower titers and qP compared toTetR-GS KO cell lines that were selected without the added pressure ofexpressing mAb_A (FIG. 23A, compare lane 9 to lanes 1, 3, 5, 7). Allpools maintained high viabilities up to day 6 of production, after whichwe started to see a decline in cell growth and viability in some celllines (FIG. 23B). Additional production cultures with these pools inproprietary production medium and feeds achieved substantially hightiters of up to 4 g/L and qP values up to 28 pg/c/d (FIG. 27A). Thosecultures selected in the absence of dox had the highest titers and qPvalues. These data indicate that the highest titer mAb expressing poolswere selected in the absence of the inducer.

Balanced LC/HC ratios correlates to increased titers and specificproductivity (qP). The mAb_A LC and HC transcript levels were analyzedby qPCR to gain insight into the increased titer and qP we observed whenwe utilized pJVec_5 compared to pJVec_4. We focused on 6F5 pools becausethat cell line gave us the highest titers and qP among the ones thatwere tested (FIG. 23A). Wild type GS KO hosts were also analyzed as acontrol. A 6F5 −Dox pool was used as a reference sample (circle, FIG.24A). We saw a positive linear relationship between qP and both LC andHC transcript levels, although the level by which LC increases is morethan that of HC (FIG. 24A, note the difference in scale). The LC/HCratio on average was similar for the induced 6F5 pools and the GS KOpools transfected with pJVec_5 vector (2.2, 1.8 and 2.3). The LC/HCratio of uninduced 6F5 was lower as would be expected from reducedtranscription from LC transcription unit interfering the HC expression.(FIG. 24B). This is in contrast to pools transfected with pJVec_4 wherewe saw that the LC/HC ratio for pools induced only during production tobe about 8.5 (FIG. 21D). Hence, consistent with our hypothesis, our dataimply that a more balanced LC/HC ratio seen with pJVec_5 pools throughusage of a more efficient polyA/terminator signal reducedtranscriptional interference and increased titers and qP. We observedthat the relative expression of LC and HC transcript levels in GS KOhost not expressing TetR were lower compared to 6F5(−)+Dox pools, aswere their qP values, further validating the use of an inducibletransposon system to find high producing pools/clones during the stablecell line development process.

Discussion We found that limiting recombinant protein expression duringcell line selection yielded higher expressing pools compared to poolsthat were selected with constitutive protein expression. This effect wasobserved for both an Fc-fusion protein and a mAb. In addition, fourdifferent TetR expressing clones displayed similar results. Themagnitude of this effect was up to approximately 1.8 fold for the mAbpools to over 2-fold for the Fc-fusion molecule. These data areconsistent with data from microbial systems where the metabolic burdenof “unnecessary” protein expression can result in selection of lowerexpressing clones.

Even innocuous proteins such as beta-galactosidase and green fluorescentprotein limit growth when expressed at sufficiently high levels inmicrobial systems. Scott et al., Interdependence of cell growth and geneexpression: origins and consequences, Science 330(6007):1099-1102(2010); Miroux, B et al., Over-production of proteins in Escherichiacoli mutant hosts that allow synthesis of some membrane proteins andglobular proteins at high levels, J. Mol. Biol. 260:289-298 (1996)).

For mammalian cells this effect has been described for toxic proteins.(See, Misaghi, S. et al., It's time to regulate: Coping withproduct-induced nongenetic clonal instability in CHO cell lines viaregulated protein expression, Biotechnol Prog. 2014; 30(6):1432-1440(2014); Jones, J. et al., Optimization of tetracycline-responsiverecombinant protein production and effect on cell growth and ER stressin mammalian cells, Biotechnol Bioeng. 91(6):722-732 (2005)).

Neither of the proteins utilized in this paper had obvious toxicity, andstable cell lines with constitutive promoters have been isolated withboth molecules (data not shown). A recent report using acumate-inducible system showed a similar result to those described inthis report where restricting expression to only the production phaseyielded pools expressing higher levels of protein compared toconstitutive expression. (Poulain, A. et al., Rapid protein productionfrom stable CHO cell pools using plasmid vector and the cumategene-switch, J Biotechnol. 255:16-27 (2017)). However, their results canpotentially be explained by the observation that their induciblepromoter appeared to be significantly more powerful than theconstitutive promoters they used for comparison.

We observed a close correlation between qP and recombinant protein mRNAlevels (FIGS. 20C and 24A). Consistent with our finding, a recent papershowed that reducing the expression of the neomycin resistance (NeoR)selectable marker mRNA improves growth and expression of a recombinantantibody. In that example, the NeoR mRNA accounted for 5.63% oftranslated mRNAs on day 3 and 5.41% on day 6. Treatment of siRNAdepleted NeoR mRNA 87-92% resulting in an increase in both VCD andtiter. (Kallehauge et al., Ribosome profiling-guided depletion of anmRNA increases cell growth rate and protein secretion, Sci. Rep. 7:40388(2017)). Fomina-Yadlin et al. also showed strong correlation betweenmRNA levels and qP for a recombinant Fc-fusion protein and up to 45% oftotal cellular mRNA levels encoded the recombinant transcript forcultures treated with chemicals that induce gene expression.(Fomina-Yadlin, D. et al., Transcriptome analysis of a CHO cell lineexpressing a recombinant therapeutic protein treated with inducers ofprotein expression, J. Biotechnol. 212:106-115 (2015)).

We did not observe substantial differences in growth during productionphase between pools selected while constitutively expressing recombinantprotein compared to those only expressing recombinant protein duringproduction phase. In fact, some of the cultures selected in the presenceof Dox achieved higher VCDs and viability in production. The increase intiter observed for cultures that were only treated with Dox duringproduction was primarily associated with an increase in specificproductivity. This phenomenon is similar to that observed with E. coliexpression, where constitutive expression leads to expressioninstability and outgrowth of mutants with reduced expression ormutations that allow the cells to tolerate high levels of proteinexpression. (Miroux, B et al., Over-production of proteins inEscherichia coli mutant hosts that allow synthesis of some membraneproteins and globular proteins at high levels, J. Mol. Biol. 260:289-298(1996); Baneyx F., Recombinant protein expression in Escherichia coli,Curr. Opin. Biotechnol. 10(5):411-21 (1999)). In the pools selected inthe presence of Dox, we hypothesize that outgrowth of lower expressingclones during the selection phase accounts for the lower expressioncompared with those selected in the absence of Dox. This is consistentwith the observation that the doubling time of cultures selected in theabsence of Dox increases when those cultures are treated with Dox. Twopractical advantages of inducible systems were apparent from this workincluding higher titers and more rapid generation of recombinant proteinexpressing pools by way of faster recovery during selection.

1-9. (canceled) 10: A recombinant expression vector, comprising: (a) afirst expression cassette, comprising: (i) a control sequencecomprising: (1) a murine cytomegalovirus (mCMV) enhancer sequence,comprising a mCMV enhancer element (mCMV-E) and a CMV promoter (CMV-P)sequence at its 3′ end, operably linked 5′ to a rat EF-1alpha intronsequence; (2) an intervening first leader sequence operably linked, 3′to the CMV-P sequence of the mCMV enhancer sequence, and 5′ to the ratEF-1alpha intron sequence; and (3) a second leader sequence operablylinked 3′ to the rat EF-1alpha intron sequence; (ii) an open readingframe encoding a first immunoglobulin subunit operably linked to thecontrol sequence; and (iii) a first polyadenylation site operably linked3′ to the open reading frame; (b) a second expression cassette 3′ to thefirst expression cassette, comprising: (i) a control sequence comprisinga promoter; (i) an open reading frame encoding a second immunoglobulinsubunit operably linked to the promoter; and (iii) a secondpolyadenylation site operably linked 3′ to the open reading frame; and(c) a transcription termination sequence 3′ to the first expressioncassette and 5′ to the second expression cassette. 11: The vector ofclaim 10, wherein the control sequence (i) of the second expressioncassette comprises: (1) a mCMV enhancer sequence, comprising a mCMVenhancer element (mCMV-E) and a CMV promoter (CMV-P) sequence at its 3′end, operably linked 5′ to a rat EF-1alpha intron sequence; (2) anintervening first leader sequence operably linked, 3′ to the CMV-Psequence of the mCMV enhancer sequence, and 5′ to the rat EF-1alphaintron sequence; and (3) a second leader sequence operably linked 3′ tothe rat EF-1alpha intron sequence. 12: The vector of claim 10, furthercomprising: (d) a third expression cassette comprising: (i) a weakconstitutive promoter, operably linked to an open reading frame encodinga selectable marker; and (ii) a polyadenylation site operably linked 3′to the open reading frame. 13: The vector of claim 12, wherein the weakconstitutive promoter is a deleted SV40 promoter. 14: The vector ofclaim 13, wherein the deleted SV40 promoter comprises the nucleotidesequence of SEQ ID NO:53. 15: The vector of claim 13, wherein thedeleted SV40 promoter comprises the nucleotide sequence of SEQ ID NO:46.16: The vector of claim 12, wherein the selectable marker is glutaminesynthetase, puromycin resistance, neomycin resistance, zeomycinresistance, or dihydrofolate reductase. 17: The vector of claim 12,wherein the selectable marker is glutamine synthetase. 18: The vector ofclaim 12, wherein the selectable marker is encoded by the nucleotidesequence of SEQ ID NO:49, or a degenerate DNA sequence. 19: A mammalianhost cell, comprising the recombinant expression vector of claim
 10. 20:The mammalian host cell of claim 19, wherein the mammalian host cell isa CHO cell. 21: The mammalian host cell of claim 19, wherein the CHOcell is a CHO-K1 cell, a DXB11 cell, or a DG44 cell. 22: A method ofproducing a protein of interest, in vitro, comprising culturing themammalian host cell of claim 19 in an aqueous medium under physiologicalconditions permitting expression of the protein of interest; andrecovering the protein of interest from the medium.